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Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.
Altschul SF, Koonin EV. Altschul SF, et al. Trends Biochem Sci. 1998 Nov;23(11):444-7. doi: 10.1016/s0968-0004(98)01298-5. Trends Biochem Sci. 1998. PMID: 9852764 Review. No abstract available.
Domain enhanced lookup time accelerated BLAST.
Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL. Boratyn GM, et al. Among authors: altschul sf. Biol Direct. 2012 Apr 17;7:12. doi: 10.1186/1745-6150-7-12. Biol Direct. 2012. PMID: 22510480 Free PMC article.
An assessment of substitution scores for protein profile-profile comparison.
Ye X, Wang G, Altschul SF. Ye X, et al. Among authors: altschul sf. Bioinformatics. 2011 Dec 15;27(24):3356-63. doi: 10.1093/bioinformatics/btr565. Epub 2011 Oct 13. Bioinformatics. 2011. PMID: 21998158 Free PMC article.
CONTACT: altschul@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: altschul@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
The construction and use of log-odds substitution scores for multiple sequence alignment.
Altschul SF, Wootton JC, Zaslavsky E, Yu YK. Altschul SF, et al. PLoS Comput Biol. 2010 Jul 15;6(7):e1000852. doi: 10.1371/journal.pcbi.1000852. PLoS Comput Biol. 2010. PMID: 20657661 Free PMC article.
PSI-BLAST pseudocounts and the minimum description length principle.
Altschul SF, Gertz EM, Agarwala R, Schäffer AA, Yu YK. Altschul SF, et al. Nucleic Acids Res. 2009 Feb;37(3):815-24. doi: 10.1093/nar/gkn981. Epub 2008 Dec 16. Nucleic Acids Res. 2009. PMID: 19088134 Free PMC article.
The effectiveness of position- and composition-specific gap costs for protein similarity searches.
Stojmirović A, Gertz EM, Altschul SF, Yu YK. Stojmirović A, et al. Among authors: altschul sf. Bioinformatics. 2008 Jul 1;24(13):i15-23. doi: 10.1093/bioinformatics/btn171. Bioinformatics. 2008. PMID: 18586708 Free PMC article.
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST.
Gertz EM, Yu YK, Agarwala R, Schäffer AA, Altschul SF. Gertz EM, et al. Among authors: altschul sf. BMC Biol. 2006 Dec 7;4:41. doi: 10.1186/1741-7007-4-41. BMC Biol. 2006. PMID: 17156431 Free PMC article.
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches.
Yu YK, Gertz EM, Agarwala R, Schäffer AA, Altschul SF. Yu YK, et al. Among authors: altschul sf. Nucleic Acids Res. 2006;34(20):5966-73. doi: 10.1093/nar/gkl731. Epub 2006 Oct 26. Nucleic Acids Res. 2006. PMID: 17068079 Free PMC article.
Protein database searches using compositionally adjusted substitution matrices.
Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK. Altschul SF, et al. FEBS J. 2005 Oct;272(20):5101-9. doi: 10.1111/j.1742-4658.2005.04945.x. FEBS J. 2005. PMID: 16218944 Free PMC article. Review.
A structure-based method for protein sequence alignment.
Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH. Kann MG, et al. Among authors: altschul sf. Bioinformatics. 2005 Apr 15;21(8):1451-6. doi: 10.1093/bioinformatics/bti233. Epub 2004 Dec 21. Bioinformatics. 2005. PMID: 15613392
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