Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins

OMICS A Journal of Integrative Biology

Volumn 15, Issue 7-8, 2011, Pages 513-521

  Kolker, Natali ^a,b   Higdon, Roger ^a,b   Broomall, William ^a   Stanberry, Larissa ^a,b   Welch, Dean ^a   Lu, Wei ^c   Haynes, Winston ^a   Barga, Roger ^c   Kolker, Eugene ^a,b,d  

^a SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

^b SEATTLE CHILDREN S HOSPITAL   (United States)

^c MICROSOFT RESEARCH   (United States)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; FUNCTIONAL GROUP; PROTEIN KINASE;

AMINO ACID SEQUENCE; ARTICLE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; SENSITIVITY AND SPECIFICITY;

DATABASES, PROTEIN; PROTEINS;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 79961233639     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2011.0101     Document Type: Article

References (14)

1. 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.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402. (Pubitemid 27359211)
3. Apweiler, R., Martin, M.J., O'Donovan, C., Magrane, M., Alam- Faruque, Y., Antunes, R., et al. (2010). The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38, D142148.
4. Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., et al. (2005). The Universal Protein Resource (UniProt). Nucleic Acids Res 33, D154-D159. (Pubitemid 40207850)
5. Hartigan, J. (1975). Clustering Algorithm. New York: JohnWiley & Sons.
6. Hartigan, J. (1981). Consistency of single linkage for high-density clusters. Am Stat 76, 388-392.
7. Hastie, T., Tibshirani, R., and Friedman, J.H. (2003). The Elements of Statistical Learning (corrected edition). New York: Springer.
8. Jain, A., and Dubes, R. (1988). Algorithms for Clustering Data. Englewood Cliffs, NJ: Prentice-Hall.
9. Li, L., Stoeckert, C.J., and Roos, D.S. (2003). OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13, 2178-2189. (Pubitemid 37161775)
10. Louie, B., Higdon, R., and Kolker, E. (2009). A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PLoS ONE 4, e7546.
11. O'Brien, K.P., Remm, M., and Sonnhammer, E.L. (2005). Inparanoid: A comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33, D476-D480. (Pubitemid 40207918)
12. Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., and Wu, C.H. (2007). UniRef: Comprehensive and non-redundant Uni- Prot reference clusters. Bioinformatics 23, 1282-1288. (Pubitemid 47050545)
13. Tatusov, R., Koonin, E., and Lipman, D. (1997). A genomic perspective on protein families. Science 278, 631-637. (Pubitemid 27464953)
14. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., et al. (2003). The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4, 41.