Finding Homologs in Amino Acid Sequences Using Network BLAST Searches

BLAST, Basic Local Alignment Search Tool is used more frequently than any other biosequence database search program. The purpose of this unit is not only to show how to run searches on the Web, but also to demonstrate how to fine‐tune arguments for a specific research project. It also offers guidance for interpreting results, handling statistical significance and biological relevance issues, and selecting complementary analyses. This unit covers three classes of the BLAST program: standard protein‐to‐protein searches, translated searches when either the query or the database consists of nucleotide sequences translated into proteins, and finally programs for comparing two sequences (as opposed to searching one sequence against a database of sequences).

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