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A Randomized Controlled Trial of Routine Shave Margins Versus Standard Partial Mastectomy in Breast Cancer Patients
This study is ongoing, but not recruiting participants.
Yale University
Information provided by (Responsible Party):
Yale University
ClinicalTrials.gov Identifier:
First received: September 29, 2011
Last updated: September 1, 2016
Last verified: September 2016
- Full Text View
- Tabular View
- No Study Results Posted
- Disclaimer
- How to Read a Study Record
This research study is designed to look at whether the routine use of shave margins (by taking extra tissue at the time of partial mastectomy surgery) will reduce the chances of having positive surgical margins requiring another surgical procedure, and whether this affects the long-term chances of getting cancer back in your breast.
Condition | Intervention |
Breast Cancer |
Procedure: Shave margins Procedure: No Shave Margins |
Study Type: | Interventional |
Study Design: | Allocation: Randomized Intervention Model: Parallel Assignment Masking: Open Label Primary Purpose: Treatment |
Official Title: | A Randomized Controlled Trial of Routine Shave Margins vs. Standard Partial Mastectomy in Breast Cancer Patients |
Resource links provided by NLM:
Further study details as provided by Yale University:
Primary Outcome Measures:
- Optimal surgical treatment [ Time Frame: 12 months ]To determine whether routine shave margins in breast cancer patients undergoing partial mastectomy will result in more optimal surgical treatment of breast cancer patients, as defined by reduced positive margin rates
Secondary Outcome Measures:
- Cosmesis [ Time Frame: 12 months ]To determine the effect of routine shave margins on cosmesis
- Operative time [ Time Frame: 12 months ]To determine the effect of routine shave margins on the time in the operating suite.
- Volume of tissue resected [ Time Frame: 12 months ]To determine the effect of routine shave margins on the volume of tissue resected.
Enrollment: | 251 |
Study Start Date: | October 2011 |
Estimated Study Completion Date: | October 2016 |
Primary Completion Date: | August 2014 (Final data collection date for primary outcome measure) |
Arms | Assigned Interventions |
Experimental: Shave Margins |
Procedure: Shave margins
Partial mastectomy with shave margins.
Active Comparator: No shave margins |
Procedure: No Shave Margins
Partial mastectomy without shave margins.
Ages Eligible for Study: | 18 Years to 90 Years (Adult, Senior) |
Sexes Eligible for Study: | Female |
Accepts Healthy Volunteers: | No |
Inclusion Criteria:
- Breast cancer, stage 0-3, deemed a surgically appropriate candidate for partial mastectomy with planned procedure for the same.
- Women ≥ 18 years of age.
- Ability to understand and the willingness to sign a written informed consent document.
Exclusion Criteria:
- Patients who have received previous neoadjuvant chemotherapy
- Patients who require a total mastectomy
- Known metastatic breast cancer.
Contacts and Locations
Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study.
To learn more about this study, you or your doctor may contact the study research staff using the Contacts provided below.
For general information, see Learn About Clinical Studies.
Please refer to this study by its ClinicalTrials.gov identifier: NCT01452399
Please refer to this study by its ClinicalTrials.gov identifier: NCT01452399
United States, Connecticut | |
Yale University School of Medicine | |
New Haven, Connecticut, United States, 06510 |
Sponsors and Collaborators
Yale University
Principal Investigator: | Anees Chagpar, M.D. | The Breast Center -- Smilow Cancer Hospital at Yale-New Haven |
More Information
Publications automatically indexed to this study by ClinicalTrials.gov Identifier (NCT Number):
Additional relevant MeSH terms:
ClinicalTrials.gov processed this record on March 27, 2017
Publications automatically indexed to this study by ClinicalTrials.gov Identifier (NCT Number):
Responsible Party: | Yale University |
ClinicalTrials.gov Identifier: | NCT01452399 History of Changes |
Other Study ID Numbers: |
1107008825 |
Study First Received: | September 29, 2011 |
Last Updated: | September 1, 2016 |
Additional relevant MeSH terms:
Breast Neoplasms Neoplasms by Site Neoplasms Breast Diseases Skin Diseases |
ClinicalTrials.gov processed this record on March 27, 2017


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LA Street Racers Plead No Contest To ManslaughterKaren Gary Balyan pleaded no contest to vehicular manslaughter with gross negligence, assault with a deadly weapon and acknowledged fleeing the scene of the deadly crash.
Man Charged With Vehicular Manslaughter In Crash That Killed Grandmother, GranddaughterA man was charged Monday with two counts of vehicular manslaughter in connection with a hit-and-run crash that killed a 54-year-old woman and her 2-year-old granddaughter in Irvine.
Woman Sentenced After Pleading No Contest To Killing 2 Friends In 2013 CrashA 24-year-old woman was scheduled to be sentenced Tuesday for the death of two friends killed in a 2013 crash on the 110 Freeway.
Man Charged In Connection With Crash That Killed CentenarianAuthorities say a 41-year-old man has been charged in connection with a crash that killed a 101-year-old pedestrian in Boyle Heights.
Ontario Woman Gets 6 Years For 2013 Fatal DUI CrashAuthorities Friday said a 21-year-old woman, who was convicted of gross vehicular manslaughter, has been sentenced to six years in state prison.
Driver Pleads No Contest To Killing 2 Friends During Birthday CelebrationLos Angeles County authorities say a driver involved in a crash that killed two passengers and seriously injured two others pleaded no contest to two counts of vehicular manslaughter.
Man Found Guilty In Crash That Killed Road Workers Yocio Jonathan Gomez was found guilty Friday of second-degree murder, gross vehicular manslaughter while intoxicated and other charges.
Girl, 16, Killed After Suspected DUI Driver Plows Into Palmdale ApartmentA 16-year-old girl was killed early Sunday morning after a suspected drunken driver plowed his vehicle into an apartment complex in Palmdale, authorities said.
Family Seeks Justice For Honeymooner Killed In Venice Car RampageA preliminary hearing is set to begin Tuesday for the suspect involved in August's deadly vehicular rampage along the Venice Beach boardwalk, which claimed the life of a young woman on her honeymoon.
Arrest Made In Oxnard Fatal Hit-And-RunA woman has been arrested in connection with a fatal hit-and-run crash that took place in Oxnard last month, police said.
LAPD Looking For Hit And Run Driver Who Struck And Killed Man At Valet StandLAPD is on the search for a hit and run driver who struck and killed a young man at a valet stand early Sunday.
Victim's Family Reacts To News That Daughter Of LAPD Sgt. Free Until OctoberThe family of a man allegedly struck and killed by the daughter of a veteran Los Angeles police sergeant are struggling with news that the suspect is free, and not due in court until October.

subset: commoncrawl


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Quick ViewRifle Paper Co. Roll Wrap Pack of 3 Rolls - Floralby Rifle Paper Co.In stock onlineNot available in stores$29.00
Quick ViewNeon Cheers Wreath Gift Bag - Largeby IndigoOut of stock onlineAvailable in stores$5.50$2.75
Quick ViewSAVE 50%Pink Celebrate Gift Bag - Largeby IndigoIn stock onlineAvailable in stores$5.50$2.75
Quick ViewEnjoy Little Things Gift Bag - Smallby IndigoOut of stock onlineAvailable in stores$3.50$1.75
Quick ViewPink Floral Extra Large Gift Bagby IndigoOut of stock onlineNot available in stores$7.00$2.00
Tips for store searching: Check that you entered your information correctly. If your postal code might be further than 25kms from a store, try entering a city name instead. If there are no matches in your city, try the next closest major city.


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Lessons on how to take your denim street style to the next level
Mar 23, 2017 | By Samuel Trotman
Since 2004, Berlin retailer DC4 has been specializing in highly exclusive Japanese denim and hard-to-find specialities. While Berlin has always had its finger firmly on the pulse of premium denim, DC4 recognized the gap for the growing interest in Japanese heavy-weight denim labels.
Over the past eight years in business, owner Cizmek has built a brand portfolio including some of the world's finest denim producers including Studio D'artisan, R.J.B, Pure Blue Japan, The Flat Head, Iron Heart, and Samurai Jeans. In addition to stocking limited edition jeans, the store regularly releases exclusive collaborations with labels stocked in the store. Previous collabs included Flat Head, Samurai, and Iron Heart, offering extra-heavy denim.
In December 2011, Cazmek relocated the original DC4 outlet in Münzstrasse to one of the oldest buildings in Torstraße. The new no.95 location sits alongside contemporary menswear boutiques like No.74 and Soto, as well as hot-spots like Trust and Berlin's Soho House. The store's interior is entirely based on Cazmek's passion for denim with memorabilia, fan magazines, and books. Much of the interior stays true to the aesthetic of the former shop. One key features is the red brick walls that have been resurrected through the crumbled plaster. Industrial girders, steel rails, and original oakwood furniture further compliment the raw products on display throughout the 200 square meter space.
With a selection of dry and heavy denims, DC4 now offers a special soaking service for the shrink-to-fit jeans, as well as chain-stitching using their original 1940s Union Special 43200. They are also offering an indigo dyeing service and customized embossing on leather patches.
Check out Denimhunters exclusive interview with Daniel, as well as the store's Tumblr and webstore for more info. Below is a short video from their collaboration launch with The Flat Head earlier this year where you can take a closer look inside the store and get a sense of their aesthetic values.
DC4 & The Flat Head – Japanese Denim Party from DC4 Berlin on Vimeo.
DC4 Berlin
Torstr. 95
10119 Berlin
Know what's next. Become a WGSN member today to benefit from our daily trend intelligence, retail analytics, consumer insights and bespoke consultancy services.
Get more Denim insights as a WGSN subscriber


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Archive Three 2005 - 2009
A representative listing of activities of the Order (or Sisters) of Perpetual Indulgence, Sydney House over the years in Sydney since it's inception in 1981.
For the sake of historical reference and accuracy, Sr Archives has noted the details of the source[s] of the information. Please folow Media Links to view a selection of event images
Please Note! Many of the Listed links in this archive are still undergoing renovation so remain inactive. They will become active in the fullness of time as they are completed. Please check back from time to time.
Kylie Canapés & Cocktails
History Walk - Kings Cross & Surrounds
Blessing the Fleet - Store Beach
This website is fondly dedicated to the memory of Sister Carmen Get It - (15/4/1959 - 5/5/2006) and to all those Sisters of the Sydney House who have passed on. Send mail to Sister Web for questions, comments, general feedback, or to report broken links. © Order of Perpetual Indulgence, Sydney House - Last Modified 12th March 2017


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The Working Men's College, in Camden, north London, which boasts John Ruskin, Dante Gabriel Rossetti and Charles Kingsley among its former staff, is the focus of a clash between a philanthropic educational tradition in which teachers once worked for free, and the harsh reality of modern further-education funding.
The battle to dictate the identity of the college in the next millennium has pitched a group of staff, claiming an ally in the ghost of the institution's Christian Socialist founder Frederick Maurice, against the principal, Lord McIntosh of Haringey, Labour's deputy spokesman in the House of Lords.
The row centres on plans approved by the college corporation, a board of trustees and directors, for a fundamental shake-up of the way the institution is governed. The proposal is for the present system, in which the corporation oversees the college's trust funds but delegates educational and policy matters to an elected council of staff and students, to be replaced with a single governing body.
The rebels claim the move, which they hope to challenge in the courts, is undemocratic and out of keeping with the founder's ideals since it would leave no more than one-third of seats on the new body for teachers and students. But Lord McIntosh and the college's warden, Evelyn Murray, insist that a change is essential if the tradition of providing education for people with little access to other forms of study is to be continued.
Malvern Hostick, art teacher, college council member and a critic of the reforms, fears they will destroy a key aim of the founder who saw students taking control of their studies. "FD Maurice and his contemporaries felt teachers and students should learn from each other, and that students should eventually set their own curriculum," he said. "I think they would be rather dismayed that, thanks to market forces, we are going back to an autocratic system."
The principal and warden give short shrift to the rebels' claims to speak for the founder. The college, which today has more than 2,000 students, two-thirds of them women, has long left behind its tradition of unpaid teaching, and has only two such staff left, Ms Murray says. "In its heyday, the lecturers were civil servants, lawyers or clergymen who worked in the morning and then came to college for a meal and a bit of teaching in the evening. Nowadays, ambitious barristers are on the next plane to New York."
A report last year by inspectors from the Further Education Funding Council, which finances 15 per cent of the college's courses, praised some teaching but found "significant weaknesses" in governance, management and quality assurance. Following the report, the corporation set up working groups to devise an action plan, which included the new governance.
Lord McIntosh says the present system does not work. "Very few students or staff stand for election and the corporation and council don't actually do the things that are necessary - they don't make difficult decisions on the budget or establish the educational programme." The college had interpreted the founders' intentions in the language of the Nineties, and now offered academic qualifications and leisure courses, he said.
The college's class of '97, while doubtless as hungry for knowledge as its forbears, as yet knows little of the dispute raging beneath the institution's William Morris-designed ceilings. "I don't know about the politics," music student Richard Leskin said. "I just come for the course. But I would be worried if the fees went up."
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I love perfumes, lotions, candles and air fresheners. Anything that gives a sweet and welcoming aroma really. I especially love when a scent can define a moment in time or a period of my life.
I know, I know. Malibu Musk is a fragrance from two decades ago - but I always keep a Body Spray of the scent on hand.
It's a fun scent that takes me back to high school. Most specifically it takes me to my days as a high school cheerleader. It seemed every cheerleader in our league used Malibu Musk and the cheerleader 'locker room" {we never actually had a locker room... but classrooms or abandoned classrooms} always smelled of this beautiful scent.
Another perfume I love to keep on hand is Miracle by Lancome. This isn't a great picture - so you can't see the name - but it is a pink tinted perfume that I began wearing around the time that I met my husband.
I have continue to wear it since that Fall day in 2001 when our paths crossed and I've never tired of it. It hasn't become so common that I no longer recognize it's sweet scent - but it reminds me of that sunny and brisk Fall moment.
With each spritz I am taken back to my college days and the excitement of meeting someone so incredible and who took my breath away.
This scent is also not a fancy fragrance - but one that sticks out for me. I purchased it at I believe a CVS a year or so ago. It was Spring time and the earth was beginning to shows signs of blooming after a cold and icy Winter.
I used the lotion most of the Spring and then forgot about it. I happened across it earlier this year and it immediately brought me back to the Spring of 2011.
What scents take you back to a memorable time in your life?


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Christian Counselor
Harmony Moses, MA, LPC
Licensed Professional Counselor
1809 K Ave, Plano, TX 75074
As a Christian, Harmony knows first-hand how important it is for Christians to find a therapist who shares the same belief system. Although not Biblically trained, she is happy to accomodate as little or as much Christianity and spirituality as each individual client needs. For many Christians having a 'Faith-based' counselor is very important when researching and finding the right fit in a counselor.
Christian Counselor
Marvin Schick, MA, LMFTA
Licensed Marital and Family Therapist Associate
2001 W. Plano Parkway Suite 2300 - The Hope Center, Plano, TX 75075
The Bible is God's instruction to Christians on so many topics. A most valuable set of topics is of course, family development and marital satisfaction. As a Christian Minister I approach counseling with an integration of biblical and clinical principles. One informs the other. The Bible is silent on many topics and theologically, one must not attempt to make doctrine out of silence. If you have spiritual questions-- as they relate to your faith and counseling goals, I also happen to be trained to help guide you through your hard questions about the Christian faith and together we can find the answers that Christ wants to pour into your life.
Christian Counselor
Daniel Gowan, M.Div., M.A., LCDC, LPC-S
Licensed Professional Counselor Supervisor
4975 Preston Park Blvd., Suite 790, Plano, TX 75093
When people of faith claim a connection to their God, they benefit from using a counselor that can frame their struggles in words that are reflected in their faith. With an understanding that our lives fall under a Creator they are connected to, it is important that the counseling process acknowledge, support and guide in light of this connection. I have been ordained as Minister of Word and Sacrament in the Presbyterian Church (U.S.A.). I trained at both Perkins School of Theology (at SMU) and Amberton University. My counseling practice is a "Validated Ministry" within Grace Presbytery.
Christian Counselor
Center for Family Counseling
5228 Tennyson Parkway, Bldg. 3, Suite 102, Plano, TX 75024
The Center for Family Counseling delivers developmentally appropriate and culturally sensitive counseling services for families, couples, adults, adolescents, and children undergoing varying life circumstances, while providing SMU counseling graduate students with meaningful training experience via supervised therapeutic interactions. Counseling students offer counseling services for individuals and groups seeking to enhance their overall life functioning, interpersonal relationships, self-understanding, and career satisfaction for optimal well-being.
Christian Counselor
David Ashburner, MA, LPC, CSAT, CHFP
Men and Couples Counselor
5801 W Plano Pkwy, Plano, TX 75093
Men, if you are looking for a counselor that works from a Christian base, and, is not going to try to shame you, I may be a good fit for you. Too often we focus only on the shame we feel for what we have or have not done, when there is much more that God offers: there is forgiveness, healing, and serenity for each of us. Why not claim these for yourself? Call me.
Christian Counselor
Dolores Guilliod, MA, LPC
Licensed Professional Counselor
2001 W. Plano Parkway, Suite 2300, Plano, TX 75075
The Word of God states that "you shall know the truth and the truth shall make you free". (John 8:32). As a Christian counselor I rely on the power of the Lord, Jesus Christ to do what man cannot do in and of self. The Word of God is the foundation of my practice and all therapeutic approaches utilized are filtered through the Word of God. With the client's permission, scripture and prayer are utilized in the counseling session. You are never alone on your counseling journey and as we put God in the process, we can rest in the hope that He makes everything beautiful in His time.
Christian Counselor
Paul Myers, MA. LPC
Licensed Professional Counselor
704 East 15th street, Plano, TX 75074
Do you ever feel empty inside? Life without God or spirituality seems very meaningless. Its such a large part of who we are it would be difficult to ignore. Counseling from a spiritual perspective can enhance your spiritual development and bring meaning to your life that nothing else can provide. Together we can learn and grow and have the spiritual maturity we all desire.
Christian Counselor
Lisa Powell, PhD., LPC-S, LMFT
Marriage and Family Therapist
5601 Democracy Dr., Suite 135, Plano, TX 75024
I believe that any couple who seeks counseling has a marriage that can be saved. This is especially true with Christian couples who use Biblically based beliefs in their marriage. These principles include love, compassion, respect and joy in their intimate relationship. My Christian approach to counseling incorporates principles found in the new testament to help the couple live a genuine, faith filled life with their spouse.
Christian Counselor
Andrea Schultz, M.Ed., LPC-S, RPT-S
Licensed Professional Counselor, Registered Play Therapist, Board-Approved Supervisor
2001 W. Plano Parkway, Suite 1400, Plano, TX 75075
As a Christian myself, I understand how your faith impacts the way you see the world and how you approach the challenges in life. For more than 25 years I've helped individuals and families successfully overcome those challenges. By applying sound psychological principles within the framework of your Christian faith, we'll work together to help you resolve problems, achieve your goals and restore a sense of peace and hope for your future.
Christian Counselor
Bob Good, Bob Good, M.A., Th.M., LPC-S
Licensed Professional Counselor
704 East 15th Street, #104, Plano, TX 75074
I am purposefully passionate in providing quality psychotherapy from a Christian perspective that influences the treatment of psychological, emotional, and mental health issues. To this end, I am committed to glorify God by using His Word in a professional understanding manner without legalism. I Believe that each person has the innate ability for personal growth and wholeness. I use biblical principles as a method to help you learn new skills and find more choices so as to manage life's changes with a broader range of solutions for recognizing your strengths. I Thoughtfully affirm and carefully follow the morals of the Christian faith and the ethics of the professional governing boards.


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MICROS Acquisition Makes Oracle Leading Retail POS Provider By Boston Retail Partners | July 07, 2014
With the pending acquisition of MICROS, Oracle will become the new leader in retail POS software according to Boston Retail Partners' 2014 POS/Customer Engagement Survey results. Combined, the two companies account for 19% of the retail POS software installation base. Oracle's largest acquisition since it acquired Sun Microsystems in 2010 demonstrates the attractiveness of industries it considers to be ripe for technology transformation and growth. This move sparks several questions that are worthy of debate: What changes in technology make retail/QSR/hospitality attractive enough for Oracle to invest $5.3 billion? How will the combination of Oracle and MICROS truly benefit retailers? How will SAP respond to this move? Will they make a similar acquisition, and if so, what company would be a good fit? "The retail industry is on the verge of a significant transformation from a customer engagement and technology perspective, which makes it a compelling investment opportunity for companies like Oracle," stated Walter Deacon, Principal, Boston Retail Partners. "Consumers will expect real-time retail capabilities that deliver a seamless shopping experience wherever, and whenever, they shop. Oracle's addition of MICROS store applications, combined with its existing enterprise, analytics, eCommerce and cloud capabilities, hold the promise to offer a complete solution making 'real-time retail' a reality. A key determinator of success, will be the integration of the two companies' commerce technologies. "Oracle has extensive capabilities and experience in enterprise retail software and the addition of MICROS expands its portfolio to become the de facto leader in retail POS software," stated Ken Morris, Principal, Boston Retail Partners. "With the advancements made in network reliability, virtual POS applications are prime for adoption in the retail space. Networks are ready to change retail as we know it – just like they transformed the banking industry with ATMs." With Oracle's enterprise cloud infrastructure, it is positioned to extend its cloud capabilities to retail store applications like POS. "Oracle and SAP have been fierce software competitors in many industries and retail is a key battleground," stated Ken Claflin, Executive Vice President, Boston Retail Partners. "It will be interesting to see if SAP responds with a similar acquisition or adds new capabilities that differentiate them from Oracle in this competitive market."


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Coleen - Who fancies a point and a laugh??
(42 Posts)While she's not my cuppa tea there are folk who regard Coleen Rooney as vaguely fashionable no?
I would like some of them to explain the following abominations to me please.
Deirdre Bar-NO
I don't......what the.....Huh?
Viscose Bon Marché special for £45
For those days nothing else will do but looking like a Poundstretcher Danny Zuko
Gypsies, tramps and thieves!
Geordie Shore
I was all set to come here and call you cruel for pointing and laughing but jeez! Thems some shocking outfits.
And the prices! Seriously, who the heck buys that shit?
OMG the printed kimono top is something else! I'm very tempted to get this for my sister for xmas just to see the look on her face.
I had to zoom in on the jumpsuit to see the birds.
She must have been paid a lot? Only explanation as to why she would wear these shockers. The blue cutaway bin bag is my favourite. All very strange!?
The tunic! Is is on a one woman mission to prove the other thread right
dear me
My PC opened the first 3 but was so obviously offended by them it won't let me see the others
see the whole collection here
Not so bad until I saw the £85 polyester jumpsuit with birds on it.
She does look suitably mortified in some of the pics doesn't she?
Why would you put a 5ft lass in a jumpsuit??
That last one!!
Her arms are fucking weird in the ugly stripy jumper. They seem to have shrunk... All bloody ugly and shit airbrushing too.
well, you wouldn't want to go anywhere near her with a flame would you? all that polyester would go up in seconds...
She's a lovely-looking girl, but jeez, those outfits are more hideous than anything Kayes Catalogue could have summoned from hell in 1982,
My God, the prices! You would think they would at least be cheap considering the vileness.
Oh my god, all those clothes are so ugly!!! And they are not even fashionable. Who are they aimed at???
Eighty five ACTUAL pounds for grim polyester?!!
I thought this was going to be about the Coleen Nolan collection here.
Which one is worse? You decide.
I like coleen and was hoping this was about the Nolan rather than the rooney! The clothes are a horror though but I feel more comfortable pointing and laughing at Nolan for some reason
Strange she hasn't actually been pictured wearing any of this shit in RL ... do they not stock it in Flannels ?
Honestly, talk about capitalising on minor celebrity - VB is one thing, but at least she would wear her own "creations", the hypocrisy in this, however, is breathtaking. waits to be proved wrong with pics of Coleen in nightclub wearing jumpsuit
Don't stand near a naked flame, Coleen! Awful awful AWFUL!
Have the Per Una Speziale designers got new jobs?
Only 97p per week....
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Connecting Families to Senior Living
Talk to a local advisor for FREE
Need help?
Last Updated: April 29, 2015
Eating alone is increasingly common for all age groups, but may be of particular concern for seniors. Cooking for one person can be harder because they have to scale down recipes, and it's also not as much fun. Instead of stimulating dinner conversation, the television becomes the other person at the table.
"Unfortunately a lot of meal choices turn out to be what's quick and easy to obtain," explains Anne Linge, a dietician at the University of Washington Medical Center in Seattle.
While many seniors are very active, others don't have the energy or ability to prepare meals for themselves. Some may have never set foot in the kitchen, or they're no longer physically able to prepare complex meals.
After her grandmother lost a considerable amount of weight in just a few months, Gretchen Kenney insisted that she move in with her and her husband, David, in Shoreline, Washington.
"She lost like 40 pounds, she just stopped eating," Kenney explains. "Part of it was her health, her arthritis; she couldn't get around very easily. She was just depressed and didn't want to eat."
After moving in with the Kenneys, her grandmother slowly put some of that weight back on.
"I make sure that she gets a much better balance," Kenney says. "Given what she wants, she would be happy with sweets and carbohydrates. She will ask for vegetables mostly because she thinks she should have them."
Inadequate nutrition can lead to a weakening of the immune system, increasing the risk of illness or infections, or contributing to mental confusion. And continued malnutrition could lead to depression, which in turn could lead to a loss of appetite-a vicious cycle.
For the elderly, other factors can contribute to malnutrition, including lack of money to buy adequate food, or transportation to the grocery store.
Linge had a client who lived directly across the street from a grocery store-but on the third floor. "She was trapped in her building because of her physical abilities and she couldn't get what she needed," Linge says. "So, when you think about your parents and their needs, think not only do they have enough income to purchase what they need, but, secondly, is shopping something they are able to do?"
Be sure to ask them if they are having difficulty with chewing or swallowing, if food tastes too bland, or if they've lost their appetite (it could be because of medications they may be taking, or possibly depression, which can have serious consequences). Also, check their refrigerator and see what kinds of food are in there, and whether any have passed the expiration date. Ask your loved one if they would prefer that you bring in groceries for them to cook, or that you cook for them.
To alleviate the burden of cooking for one, grocery store delis have a wide variety of nutritious, pre-cooked foods, such as roasted chicken and salads with raw vegetables. A whole chicken can last a senior for several meals (but it's best not to keep it for more than three or four days; after that, it may spoil). Buy a package of vegetables or meat already cut up for stir-fry, or a pre-made meatloaf that just needs to go in the oven. If they think food is too bland, enhance the flavor with olive oil, vinegars, garlic, or spices (but not salt). Cinnamon, cloves, ginger, and turmeric are also good for the digestion.
Getting together with other people-whether seniors or not-can make cooking and eating more fun.
"Sometimes seniors have been really creative and have gotten together with other seniors in their neighborhood or their building and said 'Let's get together and today I'll make the meal and tomorrow you'll make the meal,'" Linge says.
Finding a neighborhood hangout is also a good idea. "There are cafes in any community where seniors tend to gather. They will have their regulars in there who will be in there almost daily," Linge says. "Even if you're a party of one, you can see other people."
Living in a retirement home or assisted living community may help some seniors eat better.
"It makes a huge difference when you get residents sitting at a table together," explains gerontologist Ashley Kraft, the "Life's Neighborhood" Director at Aegis at Northgate a Seattle assisted living facility with Alzheimer's and dementia care. "It brings back the memories of eating with your family. What happens, especially with dementia, is they forget about the things we take for granted, knowing that we're hungry, knowing that we're thirsty, or they don't know how to explain that feeling."
While many people may not eat as well when eating alone as they would sitting down at a family meal, there are many options to ensure adequate nutrition. Whether by finding friends to eat with, using easy-to-prepare recipes, or making a change in the living situation, your loved one can still stay healthy with your help and encouragement.
Get the latest tips, news, and advice on aging and caregiving.
A Place for Mom is the largest assisted living referral service. We are paid by our participating communities, therefore our service is offered at no charge to families.
Copyright ©2017 A Place for Mom, Inc. All rights reserved.


text:
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Lot 25: Grouping of Lalique, including "Kazak" horse
Fall Auction with online and absentee bidding
by Case Antiques, Inc. Auctions & Appraisals
October 22, 2016
Knoxville , TN, USA
Live AuctionSold
Looking for the realized and estimated price?
Description: 1st item: Lalique "Kazak" horse sculpture. Retains the original label, base beneath tail inscribed "Lalique, France". 4" H x 7 1/2" W. 2nd item: Lalique "Compiegne" crystal bowl with clear and frosted molded leaf design. "Lalique, France" etched on the side. 4" H x 7 3/4" W x 6 1/2" D. 3rd item: 3 frosted Lalique crystal figures including a cherub and two female nudes. All etched "Lalique, France" to the base. 2 1/2" - 4 1/2" H. All 20th century. Estate of Jane McKinnon, Lenoir City, TN. (Additional high-resolution photos are available at www.caseantiques.com)
Condition Report: Excellent condition


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There are all sorts of cameras on the market, but if you're into taking panoramic pictures, this unusual camera might be just what you need.
We've spoken quite abit about augmented reality (AR) apps lately, but until now all of which have been based within applications. However, if you have the iPhone 4 or the latest iPod Touch, Occipital, a company that has developed a panoramic photo iPhone app that you might fancy trying out.
Continue reading »
Sony has unveiled two very non-pricey, highly affordable point and shoot Cyber-shots with high end specs. The DSC-TX1 and DSC-WX1 are both new additions to Sony's Cyber-shot range. Sony has blessed the TX1 and WX1 with a back-illuminated CMOS sensor, the Exmor R. If you're wondering why the duo will have near DSLR specs, its mainly because of its sensor. Their sensors will be based on those found in Sony's DSLRs, this promises to deliver optimal low-light performance without help from a flash or tripod – something that not many point and shoots are doing so well at the moment.
Both 10.2 megapixel TX1 and WX1 will be under the stunning budget price of $380. The $350 WX1 features the exact same G Lens, low-light optimized Exmor R CMOS sensor and Sweep Panaroma mode as seen in Sony's $500 HX1 mega zoom camera.
The LG Viewty Smart carries on the heritage of the first LG Viewty which was one of the first full touchscreen mobiles to sport a five-megapixel camera and direct video upload onto YouTube. Having sold over 6.5 million units worldwide, the second incarnation of Viewty offers even greater enjoyment while viewing and sharing, in addition to taking still and moving pictures, with a number of upgraded features in addition to its Intelligent Shot Mode. Main features of the new LG Viewty Smart GC900 include an 8 megapixel sensor with sensitivity up to ISO 1600, a higher resolution WVGA touchscreen, a more intelligent image processor and LGs easy-to-use S-Class User Interface (UI).
Checkout the video from LG below:
Sony launched this week their latest Cybershot flagship, the DSC HX1 digital camera. The most important feature of this camera is the 'sweep Panorama' technology which allows you to capture a 180 degree panoramic photograph in just 3 seconds, stunning stuff! The camera will be available from April priced at approx. $500.
More pictures following the jump….


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Just realized I am having a bit of a moment with coconut.
Newly discovered Blue Bell ice cream...(you know how much I love this stuff.)
New flavor of my favorite bubbly water...
Even my hair conditioner...
The marketing world must have decided that coconut was the new IT flavor.
Anyone else loving coconut recently?
Wednesday, June 22, 2011
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Roedig, Utz and Rutlidge, Sarah and Brown, James and Scott, Andrew (2010) Towards multiprocessor sensor nodes. In: HotEmNets '10 Proceedings of the 6th Workshop on Hot Topics in Embedded Networked Sensors. ACM, New York, n/a. ISBN 978-1-4503-0265-4
Full text not available from this repository.Abstract
Wireless Sensor Network (WSN) software is typically organized as a set of modules and depending on the application only necessary modules are selected, compiled and installed on a sensor node. This software flexibility is currently not matched by available hardware platforms. A sensor node always provides the same single microcontroller regardless of application requirements; efficiency is limited by the need to support the worst-case processing demands of the system. We argue that the central processing unit can be replaced by a number of less capable, interconnected and more specialized microcontrollers focused on specific tasks. Thus, unutilised processing hardware can easily be removed from the platform. This paper presents the results of an early experimental study into the benefits of using a multiprocessor sensor node architecture. The study shows that the desired hardware configuration flexibility can be achieved with relatively low overheads while supporting established sensor node programming concepts.
Item Type: | Contribution in Book/Report/Proceedings |
Subjects: | Q Science > QA Mathematics > QA75 Electronic computers. Computer science |
Departments: | Faculty of Science and Technology > School of Computing & Communications |
ID Code: | 42561 |
Deposited By: | ep_importer_comp |
Deposited On: | 03 Nov 2010 10:20 |
Refereed?: | No |
Published?: | Published |
Last Modified: | 28 Mar 2017 02:13 |
Identification Number: | |
URI: | http://eprints.lancs.ac.uk/id/eprint/42561 |
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Shule Aroon, Johnny Has Gone for a Soldier: the song and many versions of bits of these verses turn up inthe music of Ireland, Scotland, and across America.
This one is a beat driven take on the song by the Rooney Family of County Antrim, Northern Ireland. They're playing in the Stratchclyde Suite of Glasgow's Royal Concert Hall during Celtic Connections in January 2008.
Friday, June 6, 2008
Johnny Has Gone for a Soldier/Shule Aroon
Posted by Kerry Dexter at 6:33 AM 0 comments
Labels: The Rooney Family
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GM Yasser Seirawan Gives Seirawan Chess SimulVideo Clip 1/8 of Seirawan Chess SimultaneousYvette Nagel-Seirawan and GM Yasser Seirawan GM Yasser Seirawan, Bruce Harper, Len Molden, GM Duncan Suttles Organizers Len Molden and Bruce Harper congratulate Yasser After Simul Vancouver Chess Centre Organizers Toni and Norman GM Yasser Seirawan Relaxing After Simul Alfred Pechisker who defeated Yasser Duane Pollich, Washington State Chess Organizer Brazilian Gilmar Machado and Eduardo Moura originally from Brazil Jamie Harper who defeated Yasser Ed Enns, GM Duncan Suttles, Laura Harper, Tiffany Tang Port Coquitlam Chess Club Organizers Brent McLean and Ed Enns Brent McLean ponders a move Brian Sullivan and Clint Ballard Paul McNichol and Hugh Long Yvette watches husband Yasser play Bruce Harper Bruce Harper asks son Jamie how he's doing Laura Harper and Tiffany Tang Robin Harper, wife of Bruce, mother of Jamie and Laura Alfred realizes Yasser has dropped a piece Yasser realizes he's dropped a piece to Alfred! Yasser makes a move against Duane, his friend for over 30 years Yasser checks time, realizing that he and Yvette have a plane to catch Yasser about to move his c1 bishop and bring his elephant into play Yasser plays his bishop to f4 and puts his elephant on c1 vs. Hugh Long Bruce Harper and GM Duncan Suttles Video Clips 2-8 of Seirawan Chess Simultaneous
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text: The Northern Lights Screw Up Arctic Drilling OperationsJamie Condliffe3/10/16 3:20amFiled to: northenr lightsaurore borealisdrillingarcticengineering104EditPromoteShare to KinjaToggle Conversation toolsGo to permalink Image by NASA The Aurora Borealis are a beautiful sight—but, it turns out, they can be a real pain in the ass too. A new report explains that they can and do mess up drilling operations, especially in areas around the Arctic where they're most common. Advertisement Auroras happen when solar winds disturb the Earth's magnetosphere. As a result, charged particles—mainly electrons and protons—pour into the upper atmosphere, losing energy as they do so. The loss of energy occurs through the ionization and excitation of different constituents in the atmosphere, creating the cool colors associated with the northern lights.But research by Inge Edvardsen from the University of Tromsø suggests that the disturbances in the atmosphere can cause magnetic sensor—which most drilling operations use to determine their position—to play up. In turn, drilling can be imprecise. His research reveals that the problem gets worse the further North one drills. Advertisement What's to do? He suggest the answer is pretty straightforward: Install extra measurements systems below ground and at the bottom of the sea, where possible, to help corroborate the land-based measurement systems.[UIT via Barents Observer]Reply10 repliesLeave a reply


text:
A Poverty Trap in the Galilee
The future of the Israeli economy depends on having Haredim go out to work, and Israel must not bury this future in poverty traps in the Galilee and the Negev.
The government's failure to solve the problem of housing for the ultra-Orthodox has been going on for decades. Not enough Haredi cities and neighborhoods are being built. This leads to Haredim entering secular neighborhoods and cities, to bitter battles, and to an exacerbation of the already sensitive relations among various groups.
It is first and foremost the Haredi parties who are to blame for this failure; they have been members of almost every government in the last few decades, but did very little to solve the shortage.
There are two main reasons for the severe housing shortage among the ultra-Orthodox. One is the high birth rate. Today the Haredim need about 5,500 new housing units a year; in a decade from now they will need 12,000. The second reason is the severe poverty among the ultra-Orthodox and the prevalent custom that Haredi parents buy apartments for at least some of their children when they marry; Haredi parents buy an average of 3.5 apartments for their children. That is why the Haredi need for cheap housing is so desperate, and their willingness to live anywhere where there is cheap housing, including in the territories and in financially distressed cities, is so great.
Under the current government, Shas controls the Housing and Construction Ministry, and it is clear to its leaders that the party will be tested by its success in building a large number of apartments for Haredim, and cheaply. Ads in ultra-Orthodox and general-circulation newspapers indicate that the government is planning tens of thousands of housing units for Haredim - including 3,000 in Haredi neighborhoods in Tiberias and 2,000 in Safed. It was reported this week that the mayor of Upper Nazareth, Shimon Gapso, is lobbying to build a Haredi neighborhood of 8,000 homes in his city. The government appears likely to accept the plan and invest NIS 300 million in development. It is also planning to build new Haredi cities in Harish, at the entrance to Wadi Ara, and in the Negev town of Kasif.
Ostensibly, there is nothing wrong with the idea that many Haredim will move to the Galilee and the Negev. But only ostensibly. The assumption that the Haredim can be sent to outlying areas is based on the idea that Haredi men need only a Talmud, that they can study Torah all day and still make do. That's why the city of Betar Ilit, south of Jerusalem, was built almost entirely without places of employment. But one of the central objectives of the Israeli economy is to send the Haredim, both men and women, out to work. Sending them to live in areas distant from centers of employment, where it's not worth building factories, would therefore be shooting the economy in the foot. It means perpetuating the Haredi absence from the job market and Haredi poverty. These plans, if implemented, will ensure that most Haredi men will continue to avoid serving in the army, getting a job and earning a living.
Any plan for a new Haredi community must first be assessed on the basis of the employment opportunities it offers. Harish, which is located near Hadera and Netanya and the train lines in those cities, is definitely suitable, as is the new Haredi neighborhood planned for Lod, which is surrounded by employment opportunities. But if Upper Nazareth wants 8,000 Haredi families, let it show that it is capable of providing employment for them. And what will the ultra-Orthodox do in Tiberias, Safed or Kasif? Fish? Mine phosphate?
Pressured ministers tend to provide unsuccessful solutions. Housing Minister Ariel Atias is under heavy pressure to provide cheap housing at any cost. But we must not allow the construction of Haredi cities that will lock their residents out of the world of employment. The future of the Israeli economy depends on having Haredim go out to work, and we must not bury this future in poverty traps in the Galilee and the Negev.
The writer is the vice president of research and information at Hiddush-For Religious Freedom and Equality.
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Write a Review - Receive 50 Rewards Points!
Tell us your thoughts about Dr. Hauschka Deodorant Fresh so we can help you find the right products. With your review, you'll also receive 50 Rewards Points. Please note that it may take up to 72 hours for a review to appear on site. All reviews are subject to moderator approval.
Write a ReviewI absolutely love this product. I have used it for a long time. It is difficult to find in stores and I was so excited to find it on this cite. For me, the "Fresh" sent is by far a better choice than the "Floral". The "Fresh" scent is subtle enough that it does not interfere with perfumes. It is a great all natural product and I cant say enough good things about it. I use it year round.
I not only love wearing something that is natural and without aluminum, but also really like this Fresh scent. I bought this one and the Floral and while I like both, I like Fresh a tad more. Great product!
I left "Secret" years ago, when doubts rose about having aluminum in deodorant and have been searching ever since. I had used "Kiss My Face"-which I loved, but my skin would break out underneath my arms. But with Dr Hauschka-my breaking out days are gone. I will definitely buy this product again from LovelySkin.
This is a natural deodorant, I checked every ingredient and was satisfied that there was nothing dangerous included. Since it does not have strong chemicals - it will not stop you from sweating but this product does take care of the smell-problem. I sweat more when I am nervious or have to do public speaking - during those days I have to re-apply every 3 hours or so. Otherwise, on a normal day, I would re-apply every 6 hours. If you want to use natural safe products - then you have to get used to carrying a deodarant with you to re-apply once in a while. But this product works better than anything else I tried. Also, the smell is very nice, kind of herbal/grassy.


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Think about Loose Coupling | |
PerlMonks |
Re^4: Merge multiple BMP images into ICO filesby jimbojones (Friar) |
on Mar 22, 2007 at 15:11 UTC ( #606051=note: print w/replies, xml ) | Need Help?? |
Hi Yes, this is certainly biting back. The Eclipse "export RCP Application" button in the IDE works great. But does way too much under the hood. I'm in the process of trying to figure out what exactly it is doing so that I can automate it without having to have the entire Eclipse Platform installed everywhere I want to do a build (I should only need the libraries, which is a much small set of code). Thanks, J
In Section
Seekers of Perl Wisdom


text:
hey, i'm sorry if this has all been covered before i tried a form search and came up with nothing.
has there been an update (or replacement) for bonk and fiddle so that they will work on an intel mac?
i'm trying to get back into max again but i don't think i have a single old patch that doesn't use bonk somewhere…
thanks guys,
Olaf Matthes has ported bonk~ and fiddle~ among others.
thanks so much, your a star.
yes, a superstar.
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text:
Prof.S.Krupanidhi, M.Sc., Ph.D.,
Head, Department of Biosciences,
Coordinator UGC SAP DRS, DST FIST and DBT BIF programs
Sri Sathya Sai University,
Prasanthi Nilayam 515 134 A P, India
Email:[email protected]
An article submitted on January 14, 2009, published by Biology-Online.org on January 17, 2009.
Along with molecular tools, the in silico tools are supplementing and enriching to unravel the mysteries of genomic and proteomic analyses. The language of Perl programme conceived by Larry Wall (1987) reasonably suits as one of the best scripting languages to display a variety of diagnostic features of DNA depicted through simple exercises shown in the following pages.
Perl script is designed to visualize virtually the features of nucleotide strings. In the present endeavour, a few exercises are conceived to unravel the inherent features of DNA using perl script. The perl programme could be downloaded from internet and further the same can be installed in UNIX (kubuntu) platform. In the present book-let, the exercises began with the elementary arithmetic calculations and extended the same to the DNA string. Incidentally, DNA string is one of the best biological core materials to adopt perl programme to unfold its salient features, whose vast array of information have been deciphered over the years through various biochemical tools. The language of DNA infused with four nucleotides and in a unique species-specific combination constitutes genomic DNA and the same also happens to be the source for proteins and disease causing malformed proteins. Hence, the central dogma of transcription of gene and translation of gene products are the crux for the computer languages to percolate into the biological systems. Moreover, the number of nucleotides in any species is beyond arithmetic proportion and the number of variations i.e., polymorphism within the genes and the foot prints for the transcription factors and enzymatic machinery - are all tending to increase the complexity of the function of genomic DNA in vivo. In such a scenario, the computer programme such as perl has come to the rescue of biologists to unravel the mysteries of creation. The present book-let deals with a few exercises viz., in silico evaluation of DNA properties such as complementary strand, transcription of RNA, identification of start and stop signals, finding out percent GC and length of the each strand, concatenating two strings, joining two stings and chopping the terminals of RNA and translation of DNA genetic code into a protein string using the syntax of perl programme.
Perl is a scripting language, developed by Larry Wall in 1987, who designed perl language for UNIX environmental system. Perl is an acronym (precisely, retronym) and stands for Practical Extraction and Report Language. In the jargon of computer science, the scripting languages are often called interpreted languages. However, perl is both a compiled and interpreted language and hence facilitates to modify the perl scripts instantaneously than in any other programming languages. Perl is ubiquitous and a powerful language which assists to write structured programmes, advanced data structures and object oriented programme.
Unix (kubuntu) administrator is one of the best choices to write perl script. The first line of the script is called 'shebang' with hash and exclamation mark (#!/usr/bin/per w). The symbol '#' at the start of the line indicates that the respective line constitutes a comment. The programme lines prefixed with $ and @ constitute either commands or arguments. Two strings of random nucleotides' sequences are written in a text file as shown in Appendix. Later, executable text files are named as 'filename.pl', i.e., individual exercises. The retrieving of strings of nucleotides from the text file is done using scalar variable commands, followed by 'chomp' and 'join' functions to make the array of strings as a single string. The present conceived exercises are designed to work with one string and also array of variables. They represent scalar data and list data respectively. The simplest example chosen here is the two strings of nucleotides written in a text file "krupa.seq". A few short steps in perl programme are designed to retrieve one string to begin with and later two strings using '$' and '@' array commands respectively. The two strings are brought into one continuous line and made them joined using perl commands such as 'chomp' and 'join' respectively. Considering the joined string as a template, the following parameters of DNA are virtually derived viz., length, complementary strand, transcribed strand, substitution of 'start' and 'stop' codons, total count of nucleotides in the transcribed string, GC count, and percent of GC and chop function. The last exercise deals with the retrieving of nucleotide sequences of the gene of our choice from internet using Web sources. These exercises invariably provide an impetus for the beginners to practice the perl script to visualize in silico features of DNA.
1 |
== |
Equals |
2 |
!= |
Not equals |
3 |
< |
Less than |
4 |
> |
Greater than |
5 |
<= |
Less than or equals |
6 |
>= |
Greater than or equals |
7 |
++ |
Increment |
8 |
-- |
Decrement |
9 |
** |
Exponent |
10 |
+ |
Addition |
11 |
- |
Subtraction |
12 |
. |
String concatenate |
13 |
* |
Multiplication |
14 |
/ |
Division |
15 |
% |
Modulus |
16 |
x |
String repeat |
17 |
=> |
18 |
? , ! |
Conditional Operators |
19 |
\n |
New line |
20 |
\r |
Return |
21 |
\s |
Space |
22 |
\t |
Tab |
23 |
$! |
Error |
24 |
$_ |
Default variable |
Scalar variable stores a single (scalar) value. Perl scalar names are prefixed with a dollar sign ($), so for example, $x, $y, $z, $username, and $url are all examples of scalar variable names.
Array variable is capable of storing more than one value. The array names are prefixed by an [email protected] sign. For example @x, @y, @z. The values assigned to the array should be separated by commas or by spaces (if they are separated by spaces then the values should be prefixed with "qw"). You could also specify ranges (["a".."z"] or [1..20]). A point to note is there should be only 2 dots.
@y=("Quarter","Dime","Nickel"); Numbers don't have quotes but
strings(characters) do.
$y[1] while retrieving a value of the array you can address
them by their position in the array and placing a $ or @
in the front as it holds only one value. Here the result
is "Dime".
@z= qw(value1 value2);
@a=(0..10); Even ranges can be specified. Here the range is
from 0 to 10
Hash variable A Perl hash is similar to an ordinary array, but instead of using integer indexes, a hash uses "keys" that can take on any scalar value. These are usually strings or numbers. The Syntax is: instead of the @ operator, associative arrays use the % symbol, and rather than square brackets [], as in $myarray[0], hash elements are referenced using curly brackets {}, as in $myhash{"george"}
Subroutine is a user defined function to perform a particular or a set of tasks. The subroutine could be placed anywhere in the program body, but usually it is best to put them either at the beginning or at the end of the program
The syntax of the subroutine is defined as (as seen in line 11 of program 2):
sub <name_of_the_subroutine>{
<body of the subroutine>
Substitution is a method by which you can substitute a word with a new word. If the new word is empty, then the word is substituted by null. In other terms deleted as null has no value. The syntax for substitution is given as:
s/<word>/<new word>/<options> as in line 13 of program 3
The option are:
g – Global substitution. That is to substitute the old word
with the new word in the whole value of the variable
i – Ignore case. That is for example you can substitute the
word "bIO" to "bioinfo" and also any occurrences of
If non of the options are specified then the command substitutes only the first occurrence of the word in the variable.
Translation is a method by which you can translate a character to a new character, but you don't really substitute it. If you give a word, then each letter of the word is translated to the corresponding new letter of the new word. If the new letter is empty then the letter is substituted by null, therefore deleted.The syntax for translation is given as:
tr/<letter>/<new letter>/ as in line 6 to 9 of program 3
You can also specify range such as tr/[a-z]/[A-Z] which is used to change to uppercase.
While loop. The While Loop is used to perform an operation when the condition provided is true or in other terms the loops is executed until the condition turns false. The syntax is:
Do while loop. To create a loop that executes statements first, and then tests an expression, you need to combine while with a preceding do {} statement. For example:
$calc +=($fact*$ivalue);
}while ($calc<100);
In this case, the code block is executed first, and the conditional expression is only evaluated at the end of each loop iteration. Here we multiply $fact and $ivalue and add it to the value $calc and save the result in $calc. The condition is then checked in the end that is to execute the loop until $calc is less than 100. Once it is equal or greater than 100, the loop breaks.
Until Loop. Its syntax is:
Until the condition is met the loop keeps executing. Once the condition is met the loop breaks or exits. It is the inverse of the while loop
Do until. Here The statements are first executed and then the condition is checked. The syntax is:
$calc += ($fact*$ivalue);
} until ($calc >= 100);
Here we multiply $fact and $ivalue and add it to the value $calc and save the result in $calc. The unitl condition then checks if the $calc is greater than or equal to 100. If not the loop is again executed and terminates only when the condition is satisfied.
For loop. Its syntax is:
for(<initialization>; <condition>; <increment>){
for($i=0; $i<10; $i++){
print "the value of i is $i";
In the above example we initialize the value of $i to 0 and then print the value of 'i' until the condition is met. That is until the value of $i has become less then 10. Each time the loop is executed the value of $i is incremented by 1 due to the $i++ element. If you want to increment it by 2, then you write $i+2. $i++ is only another form for writing $i+1.
Foreach loop. The Foreach Loop is used along with arrays so that each value of the array undergoes the desired operation using an iterator. The syntax is:
Pop function. The pop function is to eliminate the last value of an array. The syntax is:
Push function. The push function is to push a value to the last position of an array. The syntax is:
push(@array, 'value');
Sort function. The sort function is to alphabetically sort the values in the array. The syntax is:
Open. The function open uses a file handler to open a file and is used for reading and writing to a file. The Open command ends with a use of another command called "close". The syntax is:
open(<file handler>, <name of the file>)
close <file handler>;
The example of the command is shown in program 8.
Chomp. It takes off the end character of a specified string ONLY if that character is a RETURN (Enter). The return character is sometimes created from input information or by the coding itself. Either way, to parse that character off, CHOMP is the command to use. IT will not affect any other characters.
Note: The RETURN character is the same as the ENTER character which is also known as a NEWLINE character. It is symbolized as \n. The syntax is:
chomp(<variable>) example:- chomp($dna); or chomp(@dna).
Chop. The next command is CHOP. This is a very similar command as CHOMP, but... it takes of the ending character of a string no matter what it is.
chop(<variable>) example:- chop($dna); or chop(@dna);
Join. It takes two arguments - a scalar variable to use as a separator (not a regular expression just a simple variable) and an array, and it returns a string that contains the elements of the array separated by the given separator. The syntax is:
This LIST could be a set of scalar variables or just an array
join(EXPR, $a,$b,$c); or join(EXPR, @array);
example:-@array=("one", "two")
print join("_", @array);
result: one_two
Split. It breaks up a string according to a separator. This is useful for tab-separated data, or colon-separated, whitespace-separated, or anything-separated data. If you can specify the separator with a regular expression, you can use split: The syntax is
@array_variable = split(/separator/, string);
Example:-my $str = "one:two:three:";
@fields = split(/:/, $str);
print @fields;
result:- one two three
Example2:- my $str = "one two three:";
@fields = split (//,$str); that is each of the three words have become a value in the array so the array has now three values and they are not anymore as a sentence.
print @fields;
result:- one two there
If elsif else. The syntax is:
if (boolean expression) {
If the boolean expression evaluates to true, the statements in the curly brackets will be executed. The curly brackets are mandatory. The boolean expression conditional can contain any one of the comparison operators covered in the next section.
Multiple conditions can be checked together using the boolean expression operators:
if ( ($x == 20) || ( ($x > 0)&&($x < 10)&&(! $x == 5) ) ){
print "x is equal to 20 or either between 0 and 10 but not 5.\n";
Conditional statements can also be extended with the elsif and else structures:
if (boolean expression 1) {
statement 1;
elsif (boolean expression 2) {
statement 2;
else {
statement 3;
Note that an if statement is followed by any number (including zero) of elsif statements, and finally an optional else statement. The statements of an elsif will be executed if its boolean expression is true, and no preceding (els)if statement's boolean expression is true. The trailing else (if present) is executed if none of the preceding statements' boolean expressions are true.
Unless. The syntax is:
unless (Boolean expression) {
Unless the Boolean expression is true, the statements within the curly brackets are executed. The "Unless" command is not a loop command.
Substr. It returns a substring of EXPR, starting at OFFSET within the string. If OFFSET is negative, starts that many characters from the end of the string. If LEN is specified, returns that number of bytes, or all bytes up until end-of-string if not specified. If LEN is negative, leaves that many characters off the end of the string.
If REPLACEMENT is specified, replaces the substring with the REPLACEMENT string.
If you specify a substring that passes beyond the end of the string, it returns only the valid element of the original string.
The syntax is:
substr EXPR, OFFSET, LEN, REPLACEMENT
substr EXPR, OFFSET, LEN
substr EXPR, OFFSET
$temp = substr("okay", 2);
print "Substring value is $temp\n";
$temp = substr("okay", 1,2);
print "Substring value is $temp\n";
result:- Substring value is ay
Substring value is kaThe objective of the program is to calculate an average for any two given numbers. Here, to begin with store the desired numbers for which averages are to be determined in scalar variables ($a, $b, $c, etc). Add any two numbers using the scalar variables and divide them by 2. The result of the calculation is stored in another scalar variable ($avg1, $avg2, $avg3, etc). Once the results are obtained and stored, we need to print the result on the screen. For this purpose we have a command called "print". The print command also includes some special commands such as "\n", "\t" for new line and tab respectively. These commands are optional.
13.5The objective of the present program is to calculate the average of any two numbers with a use of a subroutine.
As acquainted with the previous program that for finding out averages the method followed to calculate involved three steps. Here, this method envisages to use the formula once and provides three different averages. The function of the formula is done by the subroutine. So whenever we want to calculate an average, we just pass the two values to the subroutine. The subroutine calculates the average and returns the result. This way we use the formula only once.
Whenever there is a need to pass values to the subroutine we pass it by specifying the name of the subroutine and the value/s specified in brackets (as seen in line 8, 9, and 10). The subroutine collects the values by a special variable depicted as "@_" (as see in line 12).
Here in line 8, the values of $a and $b are passed to the subroutine. The subroutine gets the values and stores them in $x and $y variables for manipulation purpose. The average is then calculated using these variables and the result is stored in the $res variable. The value of $res is returned by using the command called "return". The returned value is then stored in $avg1. The same is with $avg2 and $avg3.
The Perl program is to perform concatenation of two sequences or strings. The concatenation as shown in the line 4 is just done by placing a dot. Here, the value of $DNA1 is being concatenated with the value of $DNA2. Hence, we write it as "$DNA1.$DNA2" and store the result as one complete string in $DNA3.
1. #concatenate DNA sequence
5. print"concatenated seq:$DNA3\n";
concatenated seq:AGCTGCTTGGTTGCAGCTGCCGTTGCAAA
This program demonstrates how to read contents from a file. Here we first define a scalar variable with a null value and provide the name of the file in $krupa.seq. If the file is located in the same directory where the Perl program is located then we need not specify the full path, else we need to specify full path of the file.
To open the file we use a command called "open". The "FILE" here is the file handler. The $krupa.seq contains the file name to be opened. The file is read by using the file handler.
<FILE> reads the first line in the file and stores it in the variable $dna. Here the whole line is saved as one value as the variable is a scalar. If the variable was an array, all the lines would have been read and each line would have been saved as one value in the array. This <FILE> operation is used in the while loop to read all the lines of the file in a sequence. Once the line is read and stored in $dna, we perform a chomp on the variable to remove the trailing character (enter symbol). We now concatenate the value with the existing value of $longdna and save the whole result again in $longdna. Therefore it should be written as
To make it short we write it as
That is, we have reduced it by putting ".=" which means concatenate the two values and save the result to the left hand side variable. The same is with "+=" for addition and other mathematical operations.
After every line is read, chomp and concatenated the variable $longdna contains the complete result which is printed on to the screen. The while loop ends when there are no more lines to be read, that is it has reached to the end of the file.
10. print"here is the dna:$longdna:\n\n";
here is the longdna:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGCTCCTCGGGTCGATGCGATAGCTAGCTAGATCT :
This program shows the difference in results in using scalar variables and array variables in retrieving data from a file. We first assign a file name to a scalar variable ($DNA) for our program. We then use the open command to open the file. The command <dna1> reads the first line of the file and stores the value in the scalar variable $DNA2. A scalar variable can hold only one value at a time and hence the next lines of the file are not stored in the variable instead it skips to the next line where the close command is issued. So the variable $DNA2 contains only the first line of the file.
The next test is to use an array. In line 9, the first line of the file is read and stored in the array variable @DNA2. Since the variable is an array all the lines from the file can be read and stored into this array. Each line would be stored as one value of the array. Once the file is read completely the program goes to the next line where the file is closed.
We would now like to join all the values of the array $DNA2 into one complete string. For that we would first need to remove the "enter" character at the end of each value of the array. The enter character appears each time we hit the enter key on our keyboard while writing to a file. This enter character is invisible. As all the lines are copied into the array, the values also contain this enter character. So we first remove this character by using chomp on the array. Now the array is free of the enter character. We will now join the values of the array by using a command called "join". The values of the array are joined based on 'null' ('' without any space between the quotes) as quoted in line 16. Hence there would be no value add between the values of the array. We now get one complete string from the values of the array and are stored in $DNA3. We find out the length of this variable by using a command called "length".
the sequence of krupa.seq:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC
the sequence of two strings of krupa.seq:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC
the results of chomp DNA:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC TCCTCGGGTCGATGCGATAGCTAGCTAGATCT
the result of join of two strings:
the length of two strings of DNA=66
The objective of the program is to calculate the length of the given DNA sequence and to find out the total number of dinucleotides' sequences viz GCs and ATs in the DNA.
At first we assign the value of the DNA to a scalar variable called $DNA. The length of the DNA could be obtained by just using a command called "length", result of which is stored in $length. The number of 'A' bases in the DNA are calculated by calculating the number of translations occurred by translating the 'A' to NULL in line 6. $DNA=~tr/A// translates the 'A' to NULL and by putting it in brackets and assigning it to another variable gives the number of occurrences. Similarly we get the number of 'C', 'G', 'T' bases. We then can total all the bases with the use of '+' as in normal arithmetic calculations. It is same with subtraction, multiplication and division. To count the number of GCs in the DNA (line 13) we use substitute the GC with GC itself as we just need the number of occurrences but do not want to distort the DNA. As substitution would change the DNA values but the translation does not, it only translates the value to a new one. We did not use the translation in line 13 as we have more than one letter that is a word. Similarly we would also obtain the number of ATs.
The percentage of GCs is got by using the percentage formula.
the length of DNA 40
total bases in DNA 40:
the total number of dinucleotide GC in DNA :5:
the total number of dinucleotide AT in DNA:2:
the percentage of GC:12.5:
The aim of this program is to show the use of loops like while, until, for, foreach in the Perl language. Loops are used if we need to perform a certain action for a number of times.
In the present exercise, for the "until" condition, we assign a value ("venkat") to a scalar variable $r. We then ask the user to enter a value. This value will be assigned to $i. The <STDIN> command is to tell the program that the user needs to give the value during the execution. Its abbreviation is Standard Input. When a program comes across the command, it stops and waits for the user to give the input. Once the input is given it takes the value for further execution.
So, in the 4th line the program checks whether the value of $r is present in $i (venkatraman). If the value is present it jumps to the 9th line. Otherwise it keeps printing "wrong password" and again asks the user to enter the value.
In the line 11 we used for loop to print the numbers from 0 to 9 and to print each number in a new line. We initialized the $i to 0 and specified the condition that it should be doing the loop until $i is less than 10 and incremented each time by 1. The body of for loop has a print statement to print the value of $i with a \n so that it prints it in a new line.
In line 17, each value from the array variable @ar is passed to the scalar variable $i. The value is then incremented by 2 and printed on the screen. This way all the values of the array are incremented by 2 and printed.
The while loop is used to print numbers from 0 to 5. We first initialize $k to 0 and then specify the condition ($k<5) in the While and perform the print operation and incrementing the value of $k by 1. This way the values of $k are printed from 0 to 4.
The objective of the program is to convert the DNA string to RNA string. We store the DNA in $dna. We translate the T to U in the dna and store it back in $dna. This translated DNA is then copied to $rna. The base UGC is substituted by "start" in the RNA and the number of times it has been substituted is stored in $start Count. We would need this to find the actual length of the RNA.
When we find the length of the RNA it counts every character in the RNA. Therefore, it also counts all the letters of the word "start". We need to remove this number from the total length of the RNA to get the actual length. Hence in the 10th line, we do a subtraction between the length of the RNA and the $start Count which is multiplied by 5 (as the start contains 5 letters). This actual length is stored in $length.
1. #program for transcribing
2. $dna="TGCAGCGAAATGT";
3. ($dna=~tr/T/U/);
4. $rna=$dna;
5. print"translated seq:$rna\n";
6. #Show start codon in RNA
7. $startCount=($rna=~(s/UGC/start/));
8. print"the start seq:$rna\n";
9. #length of rna
10. $length=(length($rna)-5*$startCount);
11. print"length of RNA:$length\n";
translated seq: UGCAGCGAAAUGU
the start seq: startAGCGAAAUGU
length of RNA:10The present program demonstrates pop, push, copy and sort operations on arrays. These are very straight forward commands which are very easy to understand. The array @array is filled with 4 values. Using the pop operation we remove the last value of the array. The value is stored in $array. The push operation pushes the value 'iso' into the last position of the array. The result of the new array is stored in @RE. The copy operation is done by just passing the values to the new array @array1. The sort operation alphabetically sorts all the values of the array and stores them in @RE.
1. #perform pop, push, copy and sort functions
2. #original array operations
3. @array=('ecor1', 'bam', 'hind', 'avi');
4. print"the original array:@array\n";
5. #pop operation
6. $array=pop(@array);
7. print"the pop results:@array\n";
8. #push operation
9. @RE=push(@array,'iso');
10. print"push function:@array\n";
11. #copy operations
12. @[email protected];
13. print"the copy results:@array1\n";
14. #sort operations
15. @RE=sort(@array);
16. print"the result of sort:@RE\n";
the original array:ecor1 bam hind avi
the pop results:ecor1 bam hind
push function:ecor1 bam hind iso
the copy results:ecor1 bam hind iso
the result of sort:bam ecor1 hind iso
The current program demonstrates the use of "If", "Elsif" and "Else" operations. We first store a filename in $filename. We then open the file read all the contents of the file and store them in the array and close the file. Each value of the array can be independently addressed by specifying its position. Example as shown in line 6 and 7. The 0th value (That is the first value of the array. The count starts from (0) of the array is stored in $line1 and the second value is stored in $line2.
So we now ask the user to enter any base sequence. The entered value is stored in the variable $user. Since the user hits the enter button after providing the input, the value stored in $user contains the enter character which should be removed. For that purpose we do chomp on the variable.
Now in line 13, we check if the value entered by the user is present in $line1. The expression ~/$user/ depicts that the value entered by the user can be a part of the complete string in $line1. Else you can just use $line1=$user this means to see if both are equal. But here we just enter one part (substring) of the complete string, therefore we use the expression as in line 13. If the value exists in $line1, it prints out "I found it". If it is not present in the $line1, we check in $line2. For that reason we use "elsif". The "elsif" command is used when the "if" condition returned false, that means if the above "if" condition fails. If the above "if" condition is true then the "elsif" line is not executed. So if the value entered by the user is not present in $line1 it checks if it is present in $line2. If it is there it prints "I found it in line2". If both the condition fails we then have final command called else. That means if the above "if" conditions (if and elsif) fails then the final option is "else". Here it is not checked with anything it just prints that "I did not find it"
enter the required base seq: TCT
I found it in line2
---2nd try--------
enter the required base seq: TGC
I found it
This program demonstrates of how to find motifs within a protein sequence. We first give the protein file name in line 3. We then check if the file exists by using the "Unless" command. The command does a particular operation unless the condition provided is true. That is if the condition is true it does not do the operation (in this case the print statement in line 5 will not be executed). If the condition is false it does the operation.
Once the file is ready, the contents of the file is read and stored in the array variable @protein. We then use chomp to remove the enter characters and use join to create one complete string. Now we have one big string of protein. We ask the user to enter a motif, so that we can search if the particular motif is present in the string or not. We chomp the user's input and then use the "if" condition to see if the user's motif is present in $protein. If it is present it print "I found it" else it prints "I couldn't find it". All this is put in a "do until" loop, which is from line 14 to 24. We have put it in a loop because the program keeps requesting the user to enter inputs after having finished with the previous one. When the user enters a space or simply hits the enter button, the condition in the "until" statement becomes true and hence the loop breaks.
enter a motif to search for:
I couldn't find it:
enter a motif to search for:
I found it!
enter a motif to search for:
This program aims to demonstrate a few salient features of DNA got from a file. We first store the file name in a scalar variable $DNA. We open the file and read the first line of the file and store it $DNA2. As it is scalar it holds only one value at a time and hence the other lines of the file cannot be stored. We again open the same file but this time store the contents of the file in an array so that all the contents can be read and stored as values of the array @DNA.
We do a chomp on the array (@DNA) to remove the "enter" character. The "chop" command is used to remove the last character of a particular value. We demonstrate here the use of chop. When we use chop on the array @DNA (line 16), the last character of each value of the array is deleted or removed.
We use the "join" command to make one complete string of DNA from the array values. In line 22, a complementary of the DNA string ($DNA3) is got by translating A to T, C to G, G to C and T to A and saved again in $DNA3. A point to note here is that the translation works only letter by letter and not with words. We then again translate T to U to get the RNA. We now find the length of RNA by using the command called "length". We then find out the total number of bases or nucleotides in the string by calculating the number of occurrences occurred while translating each of the nucleotides to a null value (see line 31 to 34) and totaling all the individual values.
We find out the GC percentage by calculating the number of occurrences while substituting the GC with itself, dividing it by total and multiplying it by 100. We substitute it by itself as we do not want to disturb the DNA structure but would want to know how many GCs are present. The number of adenines are already calculated in the line 31 we just do a copy to $A. We then use the substitute command to substitute the AUG and UAG to start and stop respectively.
the sequence of single strand of DNA:
the sequences of multiple strands of DNA:
the result of chomp:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTGC TCCTCGGGTCGATGCGATAGCTAGCTAGATCTT
the result of chop unction:TACTGTGGCCGTGCGTGGCTGCCGTTGCGCTG TCCTCGGGTCGATGCGATAGCTAGCTAGATCT
the result of join:
the result of complementary:
the transcribed RNA:
the length of RNA:64
the total nucleotides:in RNA:64
the total number of GC in DNA :7:
the GC percentage:10.9375
the total number of Adenines:18
the start and stop codon:
the result of chop:
The objective of the program is to read the DNA from a file or through a manual entry and convert the DNA string into a protein string. For this purpose we first use a subroutine which translates the three letter codon of DNA to the respective protein value. The subroutine contains a hash variable called "%genetic_code". This hash variable stores the protein values with their respective DNA codon. So when the subroutine gets a codon, the codon is converted to uppercase (as in line 3 with the command "uc") and then checked if the particular codon exists in this hash variable. If it exists it returns the protein value else it prints the error occurred. So at the end the subroutine returns either the protein value or the error.
We now ask the user to choose 1 for entering the DNA manually or 2 for entering the DNA through a file. If it is through manual method, the user enters the DNA value on the screen and a chomp is done on the value to remove the enter character and then stored in $dna. If it is through a file, the file is opened; the contents of the file are read and stored in an array and the values of this array then joined to form one complete DNA string and are stored in $dna.
We have used a command called "my" in front of some of the variables. This command symbolizes that the particular variable is a private variable. Which means the variable cannot be inherited by any another subroutine or program and is only applicable for that particular subroutine or program.
Now we initialize a variable $protein and $codon. We use the "for loop" to go through the DNA and get the three letter codon, save it in $codon and pass the codon to the subroutine to get the respective protein value. We then save this protein value in $protein. This way the for loop scans the DNA string until it reaches to the end.
The for loop (for(my $i=0; $i<(length($dna)-2); $i+=3)) initializes the variable $i to 0 and is limited until the last third value of the DNA by using the second element in the for loop and incrementing the value of $i by 3 for each loop. You then take the substring of the DNA by using the command in line 102 (substr($dna,$i,3)). That is you take the substring of the DNA starting from the "i" position with the length of 3. So we get the three letter codon from the DNA string. This codon is then passed to the substring which is named after "codon2aa". The codon is converted to uppercase and then the if condition is executed to see if a protein value exists with this codon and returns the protein value which saved in $protein. The next time the for loop is execute the protein value is concatenated with the existing value of the $protein and saved again in $protein, therefore getting one complete protein sequence. We can find out the length of the protein sequence by using the command called length.
Flow Chart depicting the methodology by adopting genetic code to translate DNA sting into a protein string.
9. 'TTC'=>'F', #Phenylalanine
10. 'TTT'=>'F', #Phenylalanine
11. 'TTA'=>'L', #Leucine
12. 'TTG'=>'L', #Leucine
13. 'TAC'=>'Y', #Tyrosine
14. 'TAT'=>'Y', #Tyrosine
15. 'TAA'=>'_', #Stop
16. 'TAG'=>'_', #Stop
17. 'TGC'=>'C', #Cysteine
18. 'TGT'=>'C', #Cysteine
19. 'TGA'=>'_', #Stop
20. 'TGG'=>'W', #Tryptophan
21. 'CTA'=>'L', #Leucine
22. 'CTC'=>'L', #Leucine
23. 'CTG'=>'L', #Leucine
24. 'CTT'=>'L', #Leucine
25. 'CCA'=>'P', #Proline
26. 'CAT'=>'H', #Histidine
27. 'CAA'=>'Q', #Glutamine
28. 'CAG'=>'Q', #Glutamine
29. 'CGA'=>'R', #Arginine
30. 'CGC'=>'R', #Arginine
31. 'CGG'=>'R', #Arginine
32. 'CGT'=>'R', #Arginine
33. 'ATA'=>'T', #Isoleucine
34. 'ATC'=>'T', #Isoleucine
35. 'ATT'=>'T', #Isoleucine
36. 'ATG'=>'M', #Methionine
37. 'ACA'=>'T', #Threonine
38. 'ACC'=>'T', #Threonine
39. 'ACG'=>'T', #Threonine
40. 'ACT'=>'T', #Threonine
41. 'AAC'=>'N', #Asparagine
42. 'AAT'=>'N', #Asparagine
43. 'AAA'=>'K', #Lysine
44. 'AAG'=>'K', #Lysine
45. 'AGC'=>'S', #Serine#Valine
46. 'AGT'=>'S', #Serine
47. 'AGA'=>'R', #Arginine
48. 'AGG'=>'R', #Arginine
49. 'CCC'=>'P', #Proline
50. 'CCG'=>'P', #Proline
51. 'CCT'=>'P', #Proline
52. 'CAC'=>'H', #Histidine
53. 'GTA'=>'V', #Valine
54. 'GTC'=>'V', #Valine
55. 'GTG'=>'V', #Valine
56. 'GTT'=>'V', #Valine
57. 'GCA'=>'A', #Alanine
58. 'GCC'=>'A', #Alanine
59. 'GCG'=>'A', #Alanine
60. 'GCT'=>'A', #Alanine
61. 'GAC'=>'D', #Aspartic Acid
62. 'GAT'=>'D', #Aspartic Acid
63. 'GAA'=>'E', #Glutamic Acid
64. 'GAG'=>'E', #Glutamic Acid
65. 'GGA'=>'G', #Glycine
66. 'GGC'=>'G', #Glycine
67. 'GGG'=>'G', #Glycine
68. 'GGT'=>'G', #Glycine
69. );
70. if(exists $genetic_code{$codon}){
71. return $genetic_code{$codon};
72. }
73. else{
74. print STDERR "Bad Codon\"$codon\"!!\n";
75. exit;
76. }
77. }
[email protected]:~/Desktop/bioperl$ perl dna2prot.pl
Please choose one of the following for entering the DNA sequence
Press 1 for manual entry or 2 for file
enter the sequence:-
The protein is:-
The length of the protein is:-
[email protected]:~/Desktop/bioperl$ perl dna2prot.pl
Please choose one of the following for entring the DNA sequence
Press 1 for manual entry or 2 for file
enter the filename(if it is in another folder please specify the path)
The protein is:-
The length of the protein is:-
press 1 for manual entry or 2 for file
press either 1 or 2 only
This program uses the bioperl package to connect to the internet and get a Swissprot sequence from the internet databases using the get_sequence and is saved in $seq_object. The blast_sequence blasts a sequence against standard databases at NCBI and the result of the blast is stored in $blast_result. The write_blast writes a blast report out to a file. In this case the file name is raol1.blast.
i. krupa.seq
ii.Beta-globin gene:
iii. Prot.prot
iv. IL2:
Genomic sequence in Fasta format
>ref|NT_016354.18|Hs4_16510:47920772-47925797 Homo sapiens chromosome 4 genomic contig, reference assembly
v. mRNA sequence: IL 2
>gi|125661059|ref|NM_000586.3| Homo sapiens interleukin 2 (IL2), mRNA
vi. Hemoglobin alpha 1:
Gene seq:
>ref|NT_037887.4|Hs16_37891:166679-167520 Homo sapiens chromosome 16 genomic contig, reference assembly
vii. mRNA: alpha 1
>gi|14456711|ref|NM_000558.3| Homo sapiens hemoglobin, alpha 1 (HBA1), mRNA
viii. Hemoglobin Beta Chain
>ref|NT_009237.17|Hs11_9394:4033937-4035542 Homo sapiens chromosome 11 genomic contig, reference assembly
ix. mRNA hb b-chain
>gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA
Suggested reading:
1. Randal L Schwartz, Tom Phoenix and Brian d foy, 2005, Learning perl, 4th edition, O'Reilly.
2. Brian D Foy, 2006, Learning Perl Student Workbook, 4th edition, O'Reilly.
3. Larry Wall, 2000, Programming Perl, 3rd Edition, O'Reilly
4. James Tisdall, 2001, Beginning Bioperl for Bioinformatics, 1st edition, O'Reilly
5. James D. Tisdall, 2003, Mastering Perl for Bioinformatics, 1st edition, O'Reilly
6. Ian Korf, Mark Yandell, Joseph Bedell, 2003, BLAST, 1st edition, O'Reilly


text:
A mother duck and her ducklings visited the White House Wednesday, but their trip hit a snag.
The ducklings couldn't quite get over the concrete barrier and were stuck milling about outside.
A group of uniformed Secret Service agents saw the separation and went to the ducklings' aid. They lifted each duck through the fence.
Visitors gave the agents a big round of applause afterward.
The ducks were later seen resting in the bushes.
Published at 7:50 PM EDT on Mar 21, 2012 | Updated at 9:16 AM EDT on Mar 22, 2012


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text:
PLAYING TIME: Berkman to Rangers, Soriano to Nationals
By Harold Nichols
January 17th, 2013 1:05am
Rangers sign Berkman to DH
The Texas Rangers signed Lance Berkman (1B/DH) to a one-year, $10 million contract, and he's expected to serve as their full-time DH and hit third in the lineup. It's a high risk/high reward move for the Rangers, as Berkman has the skills to be productive if he can stay healthy. Health is hardly a given, however—Berkman was limited to 32 games in 2012 by continuing knee issues.
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