Altschul SF - Search Results

1

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Schäffer AA, et al. Among authors: altschul sf. Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. doi: 10.1093/nar/29.14.2994. Nucleic Acids Res. 2001. PMID: 11452024 Free PMC article. Review.

2

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.

3

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.

4

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.

5

Protein sequence similarity searches using patterns as seeds.

Zhang Z, Schäffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF. Zhang Z, et al. Among authors: altschul sf. Nucleic Acids Res. 1998 Sep 1;26(17):3986-90. doi: 10.1093/nar/26.17.3986. Nucleic Acids Res. 1998. PMID: 9705509 Free PMC article.

6

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.

7

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.

Schäffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF. Schäffer AA, et al. Among authors: altschul sf. Bioinformatics. 1999 Dec;15(12):1000-11. doi: 10.1093/bioinformatics/15.12.1000. Bioinformatics. 1999. PMID: 10745990

8

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Altschul SF, et al. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. doi: 10.1093/nar/25.17.3389. Nucleic Acids Res. 1997. PMID: 9254694 Free PMC article. Review.

9

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

10

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.

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