Connect the dots: Exposing hidden protein family connections from the entire sequence tree

Bioinformatics

Volumn 24, Issue 16, 2008, Pages

  Loewenstein, Yaniv ^a   Linial, Michal ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL TOXIN; FISH VENOM; PROTEIN DERIVATIVE;

AMINO ACID SEQUENCE; ANALYTIC METHOD; CLUSTER ANALYSIS; CONFERENCE PAPER; CONTROLLED STUDY; CORRELATION ANALYSIS; EUKARYOTE; MICROORGANISM; MOLECULAR EVOLUTION; PFAM DATABASE; PLANT; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FAMILY; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TOXIN ANALYSIS; VALIDITY;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 49549101130     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn301     Document Type: Conference Paper

References (24)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305.
3. Doolittle,R.F. (1994) Convergent evolution: The need to be explicit. Trends Biochem. Sci., 19, 15-18.
4. Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
5. Finn,R.D. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
6. Grabowski,M. et al. (2007) Structural genomics: Keeping up with expanding knowledge of the protein universe. Curr. Opin. Struct. Biol., 17, 347-353.
7. Kaplan,N. et al. (2004) A functional hierarchical organization of the protein sequence space. BMC Bioinformatics, 5, 196.
8. Kifer,I. et al. (2005) Predicting fold novelty based on ProtoNet hierarchical classification. Bioinformatics, 21, 1020-1027.
9. Loewenstein,Y. et al. (2008) Efficient algorithms for exact hierarchical clustering of huge datasets: Tackling the entire protein space. Proc. Int. Conf. Intell. Syst. Mol. Biol., 24, i41-i49.
10. Madera,M. and Gough,J. (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res. 30, 4321-4328.
11. Mulder,N. and Apweiler,R. (2007) InterPro and InterProScan: Tools for protein sequence classification and comparison. Methods Mol. Biol. 396, 59-70.
12. Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
13. Pandit,S.B. et al. (2002) 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. Nucleic Acids Res., 30, 289-293.
14. Pearson,W.R. and Sierk,M.L. (2005) The limits of protein sequence comparison? Curr. Opin. Struct. Biol., 15, 254-260.
15. Portugaly,E. et al. (2006) EVEREST: Automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics, 7, 277.
16. Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
17. Sadreyev,R.I. and Grishin,N.V. (2004) Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics, 20, 818-828.
18. Schueler-Furman,O. et al. (2006) Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol. Sci., 27, 72-77.
19. Soding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
20. Sokal,R.R. and Michener,C.D. (1958) A statistical method for evaluating systematic relationships University of Kansas Science Bulletin 38, 1409-1438.
21. Wilson,D. et al. (2007) The SUPERFAMILY database in 2007: Families and functions. Nucleic Acids Res., 35, 308-313.
22. Wong,K.M. et al. (2008) Alignment uncertainty and genomic analysis. Science, 319, 473-476.
23. Wu,C. and Nebert,D.W. (2004) Update on genome completion and annotations: Protein information resource. Hum. Genomics, 1, 229-233.
24. Wu,C.H. et al. (2006) The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.