Uniclust databases of clustered and deeply annotated protein sequences and alignments

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D170-D176

  Mirdita, Milot ^a   Von Den Driesch, Lars ^a,b   Galiez, Clovis ^a   Martin, Maria J ^b   Soding, Johannes ^a   Steinegger, Martin ^a,c,d  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; CLUSTER ANALYSIS; INTERNET; PFAM DOMAIN; PREDICTION; PROTEIN DATABASE; PROTEIN FUNCTION; SCOP DOMAIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOFTWARE; TAXONOMY; UNIBOOST10 DATABASE; UNIBOOST20 DATABASE; UNIBOOST30 DATABASE; UNICLUST30 DATABASE; UNICLUST50 DATABASE; UNICLUST90 DATABASE; UNIREF50 DATABASE; UNIREF90 DATABASE; BIOLOGY; GENE ONTOLOGY; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PROCEDURES; WEB BROWSER;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE ONTOLOGY; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; WEB BROWSER;

EID: 85016161203     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1081     Document Type: Article

References (24)

1. The UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
2. Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2013) GenBank. Nucleic Acids Res., 41, D36-D42.
3. Koepfi, K.-P., Paten, B., O'Brien, S.J. and The Genome 10K Community of Scientists. (2015) The genome 10K project: A way forward. Annu. Rev. Anim. Biosci., 3, 57-111.
4. Zhang, G., Li, C., Li, Q., Li, B., Larkin, D.M., Lee, C., Storz, J.F., Antunes, A., Greenwold, M.J., Meredith, R.W. et al. (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346, 1311-1320.
5. Grigoriev, I.V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F. et al. (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res., 42, D699-D704.
6. Park, J., Holm, L., Heger, A. and Chothia, C. (2000) RSDB: representative protein sequence databases have high information content. Bioinformatics, 16, 458-464.
7. Li, W., Jaroszewski, L. and Godzik, A. (2002) Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng., 15, 643-649.
8. Chubb, D., Jefferys, B.R., Sternberg, M.J.E. and Kelley, L.A. (2010) Sequencing delivers diminishing returns for homology detection: Implications for mapping the protein universe. Bioinformatics, 26, 2664-2671.
9. Suzek, B.E., Wang, Y., Huang, H., McGarvey, P.B. and Wu, C.H. (2015) UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics, 31, 926-932.
10. Li, W. and Godzik, A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
11. Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A. et al. (2015) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res., 44, D279-D285.
12. Hubbard, T. J.P., Ailey, B., Brenner, S.E., Murzin, A.G. and Chothia, C. (1999) SCOP: A structural classifcation of proteins database. Nucleic Acids Res., 27, 254-256.
13. Berman, H., Henrick, K. and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
14. Hauser, M., Steinegger, M. and Söding, J. (2016) MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics, 32, 1323-1330.
15. Sjölander, K., Datta, R.S., Shen, Y. and Shoffner, G.M. (2011) Ortholog identifcation in the presence of domain architecture rearrangement. Brief. Bioinform., 12, 413-422.
16. Remmert, M., Biegert, A., Hauser, A. and Söding, J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
17. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
18. Bostock, M., Ogievetsky, V. and Heer, J. (2011) D3 data-driven documents. IEEE Trans. Vis. Comput. Graph., 17, 2301-2309.
19. Yachdav, G., Wilzbach, S., Rauscher, B., Sheridan, R., Sillitoe, I., Procter, J., Lewis, S., Rost, B. and Goldberg, T. (2016) MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics, doi:10.1093/bioinformatics/btw474.
20. Huerta-Cepas, J., Serra, F. and Bork, P. (2016) ETE 3: reconstruction, analysis and visualization of phylogenomic data. Mol. Biol. Evol., 33, 1635-1638.
21. Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
22. Lin, D. (1998) An information-theoretic defnition of similarity. In: Proc. Fifteenth Int. Conf. Mach. Learn. pp. 296-304.
23. Azuaje, F., Wang, H. and Bodenreider, O. (2005) Ontology-driven similarity approaches to supporting gene functional assessment. In: Proc. ISMB'2005 SIG Meet. Bio-ontologies. pp. 9-10.
24. Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J. et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol., 7, 539.