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Blast sampling for structural and functional analyses.

Friedrich A, Ripp R, Garnier N, Bettler E, Deléage G, Poch O, Moulinier L.

BMC Bioinformatics. 2007 Feb 23;8:62.PMID: 17319945 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein structural similarity search by Ramachandran codes.

Lo WC, Huang PJ, Chang CH, Lyu PC.

BMC Bioinformatics. 2007 Aug 23;8:307.PMID: 17716377 [PubMed - indexed for MEDLINE]Related articlesFree article

Finding homologs in amino acid sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2003 Feb;Chapter 3:Unit 3.4.PMID: 18428697 [PubMed - indexed for MEDLINE]Related articles

MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization.

Zhou CL, Lam MW, Smith JR, Zemla AT, Dyer MD, Kuczmarski TA, Vitalis EA, Slezak TR.

BMC Bioinformatics. 2006 Oct 17;7:459.PMID: 17044936 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties.

Boekhorst J, Snel B.

BMC Bioinformatics. 2007 Sep 21;8:356.PMID: 17888146 [PubMed - indexed for MEDLINE]Related articlesFree article

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

Mackey AJ, Pearson WR.

Curr Protoc Bioinformatics. 2004 Oct;Chapter 9:Unit 9.4.PMID: 18428739 [PubMed - indexed for MEDLINE]Related articles

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. Epub 2009 Jan 23.PMID: 19165315 [PubMed - indexed for MEDLINE]Related articlesFree article

Flexible sequence similarity searching with the FASTA3 program package.

Pearson WR.

Methods Mol Biol. 2000;132:185-219.PMID: 10547837 [PubMed - indexed for MEDLINE]Related articles

Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses.

Miotto O, Tan TW, Brusic V.

BMC Bioinformatics. 2008;9 Suppl 1:S7.PMID: 18315860 [PubMed - indexed for MEDLINE]Related articlesFree article

Increased coverage obtained by combination of methods for protein sequence database searching.

Webber C, Barton GJ.

Bioinformatics. 2003 Jul 22;19(11):1397-403.PMID: 12874052 [PubMed - indexed for MEDLINE]Related articlesFree article

ProtRepeatsDB: a database of amino acid repeats in genomes.

Kalita MK, Ramasamy G, Duraisamy S, Chauhan VS, Gupta D.

BMC Bioinformatics. 2006 Jul 7;7:336.PMID: 16827924 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of putative domain linkers by a neural network - application to a large sequence database.

Miyazaki S, Kuroda Y, Yokoyama S.

BMC Bioinformatics. 2006 Jun 27;7:323.PMID: 16800897 [PubMed - indexed for MEDLINE]Related articlesFree article

PISCES: a protein sequence culling server.

Wang G, Dunbrack RL Jr.

Bioinformatics. 2003 Aug 12;19(12):1589-91.PMID: 12912846 [PubMed - indexed for MEDLINE]Related articlesFree article

Bioinformatics methods to predict protein structure and function. A practical approach.

Edwards YJ, Cottage A.

Mol Biotechnol. 2003 Feb;23(2):139-66. Review.PMID: 12632698 [PubMed - indexed for MEDLINE]Related articles

Intersect: identification and visualization of overlaps in database search results.

Pegg SC, Novak WR, Babbitt PC.

Bioinformatics. 2003 Oct 12;19(15):1997-9.PMID: 14555634 [PubMed - indexed for MEDLINE]Related articlesFree article

MACSIMS: multiple alignment of complete sequences information management system.

Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O.

BMC Bioinformatics. 2006 Jun 23;7:318.PMID: 16792820 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 15509606 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting mostly disordered proteins by using structure-unknown protein data.

Shimizu K, Muraoka Y, Hirose S, Tomii K, Noguchi T.

BMC Bioinformatics. 2007 Mar 6;8:78.PMID: 17338828 [PubMed - indexed for MEDLINE]Related articlesFree article

MagicMatch--cross-referencing sequence identifiers across databases.

Smith M, Kunin V, Goldovsky L, Enright AJ, Ouzounis CA.

Bioinformatics. 2005 Aug 15;21(16):3429-30. Epub 2005 Jun 16.PMID: 15961438 [PubMed - indexed for MEDLINE]Related articlesFree article

Accelerating approximate subsequence search on large protein sequence databases.

Yang J, Wang W, Xia Y, Yu PS.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:207-16.PMID: 15838137 [PubMed - indexed for MEDLINE]Related articles