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BLAST organism cross comparison as a tool for genome closure

Motivation: Tremendous effort and interest has recently been applied to the process of genomics, the determination of the entire DNA sequence of an organism of interest to researchers. The development of new methods, as well as the increased demand for this technology, has lowered the cost of sequencing and allowed many smaller academic institutions to become actively involved in genome efforts. As a wide range of new players become involved in these projects, a new tool is also becoming available—the ever enlarging database of known sequences. It has been the goal of the program developed by this project to provide an easy to use interface for facilitating genome completion by combining a number of steps in one simple application and allowing users of any technical level the ability to use BLAST comparison as a tool for gap closure. Results: We have successfully applied this method to the Streptococcus sanguis unfinished genome for suggestion of contig alignment along gaps, and (will have) confirmed these results through the subsequent closure of the gaps with PCR conducted by the software’s designed primers. Availability: This program is available free of charge for academic use. E-mail the author to receive a copy. Contact: chaneylb@hiram.edu Supplementary Materials: Primer3 for Windows is available upon request.