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Results: 1 to 20 of 116

1.

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.

PMID:
22539666
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Homologous over-extension: a challenge for iterative similarity searches.

Gonzalez MW, Pearson WR.

Nucleic Acids Res. 2010 Apr;38(7):2177-89. doi: 10.1093/nar/gkp1219. Epub 2010 Jan 11.

PMID:
20064877
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A new bioinformatics analysis tools framework at EMBL-EBI.

Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9. doi: 10.1093/nar/gkq313. Epub 2010 May 3.

PMID:
20439314
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.

Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM.

Bioinformatics. 2000 Nov;16(11):988-1002.

PMID:
11159310
[PubMed - indexed for MEDLINE]
Free Article
5.

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.

PMID:
10745990
[PubMed - indexed for MEDLINE]
Free Article
6.

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.

PMID:
22510480
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches.

Lee MM, Chan MK, Bundschuh R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W53-6. doi: 10.1093/nar/gkp301. Epub 2009 May 8.

PMID:
19429693
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Protein domain identification and improved sequence similarity searching using PSI-BLAST.

George RA, Heringa J.

Proteins. 2002 Sep 1;48(4):672-81.

PMID:
12211035
[PubMed - indexed for MEDLINE]
9.

Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: validation.

Stevens FJ.

J Mol Recognit. 2005 Mar-Apr;18(2):139-49.

PMID:
15558595
[PubMed - indexed for MEDLINE]
10.

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches.

Lee MM, Chan MK, Bundschuh R.

Bioinformatics. 2008 Jun 1;24(11):1339-43. doi: 10.1093/bioinformatics/btn130. Epub 2008 Apr 10.

PMID:
18403442
[PubMed - indexed for MEDLINE]
Free Article
11.

COMPASS server for remote homology inference.

Sadreyev RI, Tang M, Kim BH, Grishin NV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W653-8. Epub 2007 May 21.

PMID:
17517780
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sensitivity and selectivity in protein structure comparison.

Sierk ML, Pearson WR.

Protein Sci. 2004 Mar;13(3):773-85.

PMID:
14978311
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Estimation of P-values for global alignments of protein sequences.

Webber C, Barton GJ.

Bioinformatics. 2001 Dec;17(12):1158-67.

PMID:
11751224
[PubMed - indexed for MEDLINE]
Free Article
14.

SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser.

Walsh TP, Webber C, Searle S, Sturrock SS, Barton GJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W25-9. doi: 10.1093/nar/gkn320. Epub 2008 May 24.

PMID:
18503088
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

HangOut: generating clean PSI-BLAST profiles for domains with long insertions.

Kim BH, Cong Q, Grishin NV.

Bioinformatics. 2010 Jun 15;26(12):1564-5. doi: 10.1093/bioinformatics/btq208. Epub 2010 Apr 22.

PMID:
20413635
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
18678588
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2004 Oct 28;5:171.

PMID:
15511296
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
[PubMed - indexed for MEDLINE]
19.

DescFold: a web server for protein fold recognition.

Yan RX, Si JN, Wang C, Zhang Z.

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.

PMID:
20003426
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Analysis Tool Web Services from the EMBL-EBI.

McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600. doi: 10.1093/nar/gkt376. Epub 2013 May 13.

PMID:
23671338
[PubMed - indexed for MEDLINE]
Free PMC Article

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