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Quantitative sequence-function relationships in proteins based on gene ontology.

Sangar V, Blankenberg DJ, Altman N, Lesk AM.

BMC Bioinformatics. 2007 Aug 8;8:294.PMID: 17686158 [PubMed - indexed for MEDLINE]Related articlesFree article

SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

Pandit SB, Gosar D, Abhiman S, Sujatha S, Dixit SS, Mhatre NS, Sowdhamini R, Srinivasan N.

Nucleic Acids Res. 2002 Jan 1;30(1):289-93.PMID: 11752317 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic annotation of protein function based on family identification.

Abascal F, Valencia A.

Proteins. 2003 Nov 15;53(3):683-92.PMID: 14579359 [PubMed - indexed for MEDLINE]Related articles

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

Wilson CA, Kreychman J, Gerstein M.

J Mol Biol. 2000 Mar 17;297(1):233-49.PMID: 10704319 [PubMed - indexed for MEDLINE]Related articles

ESG: extended similarity group method for automated protein function prediction.

Chitale M, Hawkins T, Park C, Kihara D.

Bioinformatics. 2009 Jul 15;25(14):1739-45. Epub 2009 May 12.PMID: 19435743 [PubMed - indexed for MEDLINE]Related articles

The relationship between protein sequences and their gene ontology functions.

Duan ZH, Hughes B, Reichel L, Perez DM, Shi T.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S11.PMID: 17217503 [PubMed - indexed for MEDLINE]Related articlesFree article

A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences.

Othman RM, Deris S, Illias RM.

J Biomed Inform. 2008 Feb;41(1):65-81. Epub 2007 Jun 27.PMID: 17681495 [PubMed - indexed for MEDLINE]Related articles

Effective protein sequence comparison.

Pearson WR.

Methods Enzymol. 1996;266:227-58.PMID: 8743688 [PubMed - indexed for MEDLINE]Related articles

Fuzzy measures on the Gene Ontology for gene product similarity.

Popescu M, Keller JM, Mitchell JA.

IEEE/ACM Trans Comput Biol Bioinform. 2006 Jul-Sep;3(3):263-74.PMID: 17048464 [PubMed - indexed for MEDLINE]Related articles

ConFunc--functional annotation in the twilight zone.

Wass MN, Sternberg MJ.

Bioinformatics. 2008 Mar 15;24(6):798-806. Epub 2008 Feb 8.PMID: 18263643 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of human protein function according to Gene Ontology categories.

Jensen LJ, Gupta R, Staerfeldt HH, Brunak S.

Bioinformatics. 2003 Mar 22;19(5):635-42.PMID: 12651722 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying protein domains with the Pfam database.

Finn R, Griffiths-Jones S, Bateman A.

Curr Protoc Bioinformatics. 2003 May;Chapter 2:Unit 2.5.PMID: 18428696 [PubMed - indexed for MEDLINE]Related articles

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.PMID: 17883866 [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

Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.

Sadreyev RI, Grishin NV.

Bioinformatics. 2004 Apr 12;20(6):818-28. Epub 2004 Jan 29.PMID: 14751996 [PubMed - indexed for MEDLINE]Related articlesFree article

FastBLAST: homology relationships for millions of proteins.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2008;3(10):e3589. Epub 2008 Oct 31.PMID: 18974889 [PubMed - indexed for MEDLINE]Related articlesFree article

Mining sequence annotation databanks for association patterns.

Artamonova II, Frishman G, Gelfand MS, Frishman D.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii49-57.PMID: 16306393 [PubMed - indexed for MEDLINE]Related articlesFree article

DWARF--a data warehouse system for analyzing protein families.

Fischer M, Thai QK, Grieb M, Pleiss J.

BMC Bioinformatics. 2006 Nov 9;7:495.PMID: 17094801 [PubMed - indexed for MEDLINE]Related articlesFree article

ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization.

Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY.

BMC Bioinformatics. 2008 Feb 1;9:80.PMID: 18241343 [PubMed - indexed for MEDLINE]Related articlesFree article

SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase.

David FP, Yip YL.

BMC Bioinformatics. 2008 Sep 23;9:391.PMID: 18811932 [PubMed - indexed for MEDLINE]Related articlesFree article