Schäffer AA - 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. 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

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. Among authors: schaffer aa. 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.

3

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: schaffer aa. 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.

4

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. Bioinformatics. 1999 Dec;15(12):1000-11. doi: 10.1093/bioinformatics/15.12.1000. Bioinformatics. 1999. PMID: 10745990

5

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: schaffer aa. Bioinformatics. 2005 Apr 15;21(8):1451-6. doi: 10.1093/bioinformatics/bti233. Epub 2004 Dec 21. Bioinformatics. 2005. PMID: 15613392

6

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. Among authors: schaffer aa. 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.

7

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: schaffer aa. 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.

8

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: schaffer aa. BMC Biol. 2006 Dec 7;4:41. doi: 10.1186/1741-7007-4-41. BMC Biol. 2006. PMID: 17156431 Free PMC article.

9

Improved BLAST searches using longer words for protein seeding.

Shiryev SA, Papadopoulos JS, Schäffer AA, Agarwala R. Shiryev SA, et al. Among authors: schaffer aa. Bioinformatics. 2007 Nov 1;23(21):2949-51. doi: 10.1093/bioinformatics/btm479. Epub 2007 Oct 6. Bioinformatics. 2007. PMID: 17921491

10

Database indexing for production MegaBLAST searches.

Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. Morgulis A, et al. Among authors: schaffer aa. Bioinformatics. 2008 Aug 15;24(16):1757-64. doi: 10.1093/bioinformatics/btn322. Epub 2008 Jun 21. Bioinformatics. 2008. PMID: 18567917 Free PMC article.

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