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Items: 1 to 20 of 152

1.

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.

Bioinformatics. 1999 Dec;15(12):1000-11.

2.
3.

Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices.

Agrawal A, Huang X.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):194-205. doi: 10.1109/TCBB.2009.69.

PMID:
21071807
4.

Domain enhanced lookup time accelerated BLAST.

Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL.

Biol Direct. 2012 Apr 17;7:12. doi: 10.1186/1745-6150-7-12.

5.

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.

Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. Review.

6.

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues.

Anand B, Gowri VS, Srinivasan N.

Bioinformatics. 2005 Jun 15;21(12):2821-6. Epub 2005 Apr 7.

7.

PISCES: a protein sequence culling server.

Wang G, Dunbrack RL Jr.

Bioinformatics. 2003 Aug 12;19(12):1589-91.

8.
9.

Strategies for the effective identification of remotely related sequences in multiple PSSM search approach.

Gowri VS, Tina KG, Krishnadev O, Srinivasan N.

Proteins. 2007 Jun 1;67(4):789-94.

PMID:
17380509
10.

PSI-Search: iterative HOE-reduced profile SSEARCH searching.

Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR.

Bioinformatics. 2012 Jun 15;28(12):1650-1. doi: 10.1093/bioinformatics/bts240. Epub 2012 Apr 25.

11.

Finding homologs in amino acid sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2003 Feb;Chapter 3:Unit 3.4. doi: 10.1002/0471250953.bi0304s00.

PMID:
18428697
12.

Benchmarking PSI-BLAST in genome annotation.

Müller A, MacCallum RM, Sternberg MJ.

J Mol Biol. 1999 Nov 12;293(5):1257-71.

PMID:
10547299
13.

Powerful fusion: PSI-BLAST and consensus sequences.

Przybylski D, Rost B.

Bioinformatics. 2008 Sep 15;24(18):1987-93. doi: 10.1093/bioinformatics/btn384. Epub 2008 Aug 4.

14.

Code optimization of the subroutine to remove near identical matches in the sequence database homology search tool PSI-BLAST.

Aspnäs M, Mattila K, Osowski K, Westerholm J.

J Comput Biol. 2010 Jun;17(6):819-23. doi: 10.1089/cmb.2008.0053.

PMID:
20583927
15.

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance.

Agrawal A, Huang X.

Bioinformatics. 2009 Apr 15;25(8):1082-3. doi: 10.1093/bioinformatics/btp089. Epub 2009 Feb 27.

16.

Fast index based algorithms and software for matching position specific scoring matrices.

Beckstette M, Homann R, Giegerich R, Kurtz S.

BMC Bioinformatics. 2006 Aug 24;7:389.

17.

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families.

Gowri VS, Krishnadev O, Swamy CS, Srinivasan N.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D243-6.

18.
19.

Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage.

Kaushik S, Mutt E, Chellappan A, Sankaran S, Srinivasan N, Sowdhamini R.

PLoS One. 2013;8(2):e56449. doi: 10.1371/journal.pone.0056449. Epub 2013 Feb 20.

20.

Fast and accurate database homology search using upper bounds of local alignment scores.

Itoh M, Goto S, Akutsu T, Kanehisa M.

Bioinformatics. 2005 Apr 1;21(7):912-21. Epub 2004 Oct 27.

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