The BLAST (Altschul et al., 1990) alignment tool has been the workhorse of genomics research for almost 30 years. While many other tools were developed during this period for performing database searches and sequence alignment, BLAST remains the tool of choice for many use cases, and continues to be actively used in many bioinformatics workflows. Despite the tremendous collective experience of the bioinformatics community with BLAST, the full functionality of this tool remains poorly understood. Here we report on a feature of BLAST that operates in a non-intuitive way and that is frequently misused in bioinformatics workflows, potentially leading to erroneous results impacting numerous scientific articles.
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NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health. BLAST® Command Line Applications User Manual Internet. Bethesda (MD): National Center for Biotechnology Information (US); 2008. (Web BLAST, command line applications, etc). The NCBI manual covers quite a few powerful and handy features of BLAST on the command line that this book does not. The programs in the BLAST+ suite can search for and against sequences in protein format (as we did for the HMMER example) and in nucleotide format (A’s, C’s, T’s, and G’s). Depending on what type the query.
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Compared to modern..
