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Sequence Similarity Searching Using the BLAST Family of Programs

Database sequence similarity searching is carried out thousands of times each day by researchers worldwide. This unit describes the BLAST (Basic Local Alignment Search Tool) family of sequence similarity search programs. It compares basic and advanced searches, discusses the BLAST algorithm, and presents the variety of databases that can be searched. Examples of various BLAST searches (e.g., BLASTP, BLASTX, BLASTN) are included. The unit also includes a discussion of different search strategies, such as filtering repeats and low‐complexity regions, and tips for analyzing genomic DNA, mRNA, and short sequences. Two unit appendices detail the BLAST parameters and sequence identifier syntax.