SUPERFAMILY 1.75 including a domain-centric gene ontology method

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  De Lima Morais, David A ^a   Fang, Hai ^a   Rackham, Owen J L ^a   Wilson, Derek ^b   Pethica, Ralph ^a   Chothia, Cyrus ^b   Gough, Julian ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC DATABASE; HIDDEN MARKOV MODEL; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; SUPERFAMILY 1.75; WEB BROWSER;

DATABASES, PROTEIN; GENES; PHENOTYPE; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 78651274743     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1130     Document Type: Article

References (33)

1. Gough,J. and Chothia,C. (2002) SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches,alignments and genome assignments. Nucleic Acids Res.,30,268-272.
2. Andreeva,A.,Howorth,D.,Brenner,S.E.,Hubbard,T.J.,Chothia,C. and Murzin,A.G. (2004) SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res.,32,D226-D229.
3. Madera,M.,Vogel,C.,Kummerfeld,S.K.,Chothia,C. and Gough,J. (2004) The SUPERFAMILY database in 2004: Additions and improvements. Nucleic Acids Res.,32,D235-D239.
4. Wilson,D.,Madera,M.,Vogel,C.,Chothia,C. and Gough,J. (2007) The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res.,35,D308-D313.
5. Wilson,D.,Pethica,R.,Zhou,Y.,Talbot,C.,Vogel,C.,Madera,M.,Chothia,C. and Gough,J. (2009) SUPERFAMILY-sophisticated comparative genomics,data mining,visualization and phylogeny. Nucleic Acids Res.,37,D380-D386.
6. The UniProt Consortium. (2010) The universal protein resource (UniProt) in 2010. Nucleic Acids Res.,38,D142-D148.
7. Eddy,S.R. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform.,23,205-211.
8. Karplus,K.,Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics,14,846-856.
9. Stamatakis,A. (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics,22,2688-2690.
10. Benson,D.A.,Karsch-Mizrachi,I.,Lipman,D.J.,Ostell,J. and Sayers,E.W. (2009) GenBank. Nucleic Acids Res.,37,D26-D31.
11. Pethica,R.,Barker,G.,Kovacs,T. and Gough,J. (2010) TreeVector: Scalable,interactive,phylogenetic trees for the web. PLoS One,5,e8934.
12. Berman,H.M.,Westbrook,J.,Feng,Z.,Gilliland,G.,Bhat,T.N.,Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The protein data bank. Nucleic Acids Res.,28,235-242.
13. Hunter,S.,Apweiler,R.,Attwood,T.K.,Bairoch,A.,Bateman,A.,Binns,D.,Bork,P. ,Das,U.,Daugherty,L.,Duquenne,L. et al. (2009) InterPro: The integrative protein signature database. Nucleic Acids Res.,37,D211-D215.
14. Rackham,O.J.,Madera,M.,Armstrong,C.T.,Vincent,T.L.,Woolfson,D.N. and Gough,J. (2010) The evolution and structure prediction of coiled coils across all genomes. J. Mol. Biol.,403,480-493.
15. Stein L.D. (2010) The case for cloud computing in genome informatics. Genome Biol.,11,207
16. Munroe,D.J. and Harris,T.J. (2010) Third-generation sequencing fireworks at Marco Island. Nat. Biotechnol.,28,426-428.
17. Flusberg,B.A.,Webster,D.R.,Lee,J.H.,Travers,K.J.,Olivares,E.C.,Clark,T.A. ,Korlach,J. and Turner,S.W. (2010) Direct detection of DNA methylation during single-molecule,real-time sequencing. Nat. Methods,7,461-465.
18. Schadt,E.E.,Linderman,M.D.,Sorenson,J.,Lee,L. and Nolan,G.P. (2010) Computational solutions to large-scale data management and analysis. Nat. Rev. Genet.,11,647-657.
19. Madera,M. and Gough,J. (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res.,30,4321-4328.
20. Barrell,D.,Dimmer,E.,Huntley,R.P.,Binns,D.,O'Donovan,C. and Apweiler,R. (2009) The GOA database in 2009-An integrated gene ontology annotation resource. Nucleic Acids Res.,37,D396-D403.
21. Velankar,S.,Best,C.,Beuth,B.,Boutselakis,C.H.,Cobley,N.,Sousa Da Silva,A.W.,Dimitropoulos,D.,Golovin,A.,Hirshberg,M.,John,M. et al. (2010) PDBe: Protein Data Bank in Europe. Nucleic Acids Res.,38,D308-D317.
22. Gough,J.,Karplus,K.,Hughey,R. and Chothia,C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol.,313,903-919.
23. Gough,J. (2006) Genomic scale sub-family assignment of protein domains. Nucleic Acids Res.,34,3625-3633.
24. Andreeva,A.,Howorth,D.,Chandonia,J.M.,Brenner,S.E.,Hubbard,T.J.,Chothia, C. and Murzin,A.G. (2008) Data growth and its impact on the SCOP database: New developments. Nucleic Acids Res.,36,D419-D425.
25. Forslund,K. and Sonnhammer,E.L. (2008) Predicting protein function from domain content. Bioinformatics,24,1681-1687.
26. Lopez,D. and Pazos,F. (2009) Gene ontology functional annotations at the structural domain level. Proteins,76,598-607.
27. Smith,C.L. and Eppig,J.T. (2009) The mammalian phenotype ontology: Enabling robust annotation and comparative analysis. Wiley Interdiscip. Rev. Syst. Biol. Med.,1,390-399.
28. Robinson,P.N.,Kohler,S.,Bauer,S.,Seelow,D.,Horn,D. and Mundlos,S. (2008) The human phenotype ontology: A tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet.,83,610-615.
29. Finn,R.D.,Mistry,J.,Tate,J.,Coggill,P.,Heger,A.,Pollington,J.E.,Gavin,O. L.,Gunasekaran,P.,Ceric,G.,Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res.,38,D211-D222.
30. Rogers,M.F. and Ben-Hur,A. (2009) The use of gene ontology evidence codes in preventing classifier assessment bias. Bioinformatics,25,1173-1177.
31. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate-A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol.,57,289-300.
32. Alterovitz,G.,Xiang,M.,Mohan,M. and Ramoni,M.F. (2007) GO PaD: The gene ontology partition database. Nucleic Acids Res.,35,D322-D327.
33. Wilson,D.,Charoensawan,V.,Kummerfeld,S.K. and Teichmann,S.A. (2008) DBD-taxonomically broad transcription factor predictions: New content and functionality. Nucleic Acids Res.,36,D88-D92.