BLAST Resources

BLAST Documentation and Help

• YouTube Playlist
• BLAST Help Manual on the NCBI Bookshelf
• Factsheet Handouts
• Web page help tab

Selected BLAST Publications

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2. PMID: 2231712.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. doi: 10.1093/nar/25.17.3389. PMID: 9254694; PMCID: PMC146917.

Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. doi: 10.1093/nar/29.14.2994. PMID: 11452024; PMCID: PMC55814.

McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5. doi: 10.1093/nar/gkh435. PMID: 15215342; PMCID: PMC441573.

Ye J, McGinnis S, Madden TL. BLAST: improvements for better sequence analysis. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W6-9. doi: 10.1093/nar/gkl164. PMID: 16845079; PMCID: PMC1538791.

Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, Raytselis Y, Sayers EW, Tao T, Ye J, Zaretskaya I. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W29-33. doi: 10.1093/nar/gkt282. Epub 2013 Apr 22. PMID: 23609542; PMCID: PMC3692093.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PMID: 20003500; PMCID: PMC2803857.