Enhanced protein domain discovery using taxonomy

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Coin, Lachlan ^a   Bateman, Alex ^a   Durbin, Richard ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CO-OCCURRENCE; DOMAIN DISTRIBUTION; HIDDEN MARKOV; LOCALISATION; PROTEIN DOMAINS; PROTEIN SEQUENCES; PSI-BLAST; TEST SETS;

AMINO ACIDS; FORECASTING; HIDDEN MARKOV MODELS;

PROTEINS;

OXYGENASE; PROTEINASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; EMBL NUCLEOTIDE SEQUENCE DATABASE; NONHUMAN; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SCOP; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; TAXONOMY; TECHNIQUE; BIOLOGY; CHEMISTRY; CLASSIFICATION; PROTEIN TERTIARY STRUCTURE; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, STATISTICAL; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SPECIES SPECIFICITY;

EID: 2942576060     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-56     Document Type: Article

References (14)

1. Krogh A, Brown M, Mian IS, Sjölander K, Haussler D: Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 1994, 235:1501-1531.
2. Durbin R, Eddy S, Krogh A, Mitchison G: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press 1998.
3. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucl. Acids Res. 2004, 32:D138-D141.
4. Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C: Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 1998, 284:1201-1210.
5. Coin L, Bateman A, Durbin R: Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc. Natl Acad. Sci. USA 2003, 100:4516-4520.
6. Eddy SR: Profile-hidden Markov models. Bioinformatics 1998, 14:755-763.
7. Hubbard TJP, Murzin A, Brenner S, Chotia C: SCOP: a structural classification of proteins database. Nucl. Acids Res. 1997, 25:236-239.
8. Chandonia JM, Walker NS, Conte LL, Koehl P, Levitt M, Brenner SE: ASTRAL compendium enhancements. Nucl. Acids Res. 2002, 30:260-263.
9. Lavaissiere L, Jia S, Nishiyama M, de la Monte S, Stern AM, Wands JR, Friedman PA: Overexpression of human aspartyl(asparaginyl)beta-hydroxylase in hepatocellular carcinoma and cholangiocarcinoma. J. Clin. Invest. 1996, 98:1313-1323.
10. Das AK, Cohen PW, Barford D: The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J 1998, 17:1192-1199.
11. Salzet M, Chopin V, Baert J, Matias I, Malecha J: Theromin, a novel leech thrombin inhibitor. J. Biol. Chem. 2000, 275:30774-30780.
12. Scaloni A, Bottiglieri C, Ferrara L, Corona M, Gurrola GB, Batista C, Wanke E, Possani LD: Disulfide bridges of ergtoxin, a member of a new sub-family of peptide blockers of the ether-a-go-go-related K+ channel. FEBS Lett. 2000, 479:156-157.
13. Swanson WJ, Vacquier VD: Extraordinary divergence and positive Darwinian selection in a fusagenic protein coating the acrosomal process of abalone spermatozoa. Proc. Natl Acad. Sci. USA 1995, 92:4957-4961.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 1997, 25:3389-3402.