메뉴 건너뛰기




Volumn 93, Issue , 2016, Pages 15-23

Enhancing protein function prediction with taxonomic constraints - The Argot2.5 web server

Author keywords

Automated protein function prediction; Gene Ontology; Semantic similarity; Taxon constraints

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DATA BASE; GENE ONTOLOGY; MATHEMATICAL ANALYSIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; SEQUENCE ANALYSIS; TAXONOMY; CLASSIFICATION; FORECASTING; INTERNET; PHYSIOLOGY; PROTEIN DATABASE; WEB BROWSER;

EID: 84953340826     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.08.021     Document Type: Article
Times cited : (42)

References (27)
  • 3
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R., Ulitsky I., Shamir R. Network-based prediction of protein function. Mol. Syst. Biol. 2007, 3:88.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 4
    • 84953357392 scopus 로고    scopus 로고
    • A survey of computational intelligence techniques in protein function prediction
    • Tiwari A.K., Srivastava R. A survey of computational intelligence techniques in protein function prediction. Int. J. Proteomics 2014, 2014:845479.
    • (2014) Int. J. Proteomics , vol.2014 , pp. 845479
    • Tiwari, A.K.1    Srivastava, R.2
  • 5
    • 84863693531 scopus 로고    scopus 로고
    • Quality of computationally inferred gene ontology annotations
    • Skunca N., Altenhoff A., Dessimoz C. Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol. 2012, 8:e1002533.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002533
    • Skunca, N.1    Altenhoff, A.2    Dessimoz, C.3
  • 7
    • 77958120670 scopus 로고    scopus 로고
    • Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
    • Deegan J.I., Dimmer E.C., Mungall C.J. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinf. 2010, 11.
    • (2010) BMC Bioinf. , vol.11
    • Deegan, J.I.1    Dimmer, E.C.2    Mungall, C.J.3
  • 8
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • UniProt: a hub for protein information, Nucleic Acids Res, 43 (2015) D204-212.
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-212
  • 11
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • Eddy S.R. Accelerated Profile HMM Searches. PLoS Comput. Biol. 2011, 7:e1002195.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 14
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 15
    • 84925267288 scopus 로고    scopus 로고
    • UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
    • Suzek B.E., Wang Y., Huang H., McGarvey P.B., Wu C.H. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 2015, 31:926-932.
    • (2015) Bioinformatics , vol.31 , pp. 926-932
    • Suzek, B.E.1    Wang, Y.2    Huang, H.3    McGarvey, P.B.4    Wu, C.H.5
  • 16
    • 49949096013 scopus 로고    scopus 로고
    • Gene Ontology term overlap as a measure of gene functional similarity
    • Mistry M., Pavlidis P. Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinf. 2008, 9.
    • (2008) BMC Bioinf. , vol.9
    • Mistry, M.1    Pavlidis, P.2
  • 17
    • 84862298784 scopus 로고    scopus 로고
    • Semantic similarity analysis of protein data: assessment with biological features and issues
    • Guzzi P.H., Mina M., Guerra C., Cannataro M. Semantic similarity analysis of protein data: assessment with biological features and issues. Brief Bioinf. 2012, 13:569-585.
    • (2012) Brief Bioinf. , vol.13 , pp. 569-585
    • Guzzi, P.H.1    Mina, M.2    Guerra, C.3    Cannataro, M.4
  • 19
    • 84916199873 scopus 로고    scopus 로고
    • Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?
    • Mazandu G.K., Mulder N.J. Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?. PLoS ONE 2014, 9:e113859.
    • (2014) PLoS ONE , vol.9 , pp. e113859
    • Mazandu, G.K.1    Mulder, N.J.2
  • 20
    • 0002016474 scopus 로고    scopus 로고
    • Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language
    • Resnik P. Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language. J. Artif. Intell. Res. 1999, 11:95-130.
    • (1999) J. Artif. Intell. Res. , vol.11 , pp. 95-130
    • Resnik, P.1
  • 21
    • 84929622388 scopus 로고    scopus 로고
    • PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment
    • Koskinen P., Toronen P., Nokso-Koivisto J., Holm L. PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment. Bioinformatics 2015.
    • (2015) Bioinformatics
    • Koskinen, P.1    Toronen, P.2    Nokso-Koivisto, J.3    Holm, L.4
  • 25
    • 84905166669 scopus 로고    scopus 로고
    • Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt
    • Huntley R.P., Sawford T., Martin M.J., O'Donovan C. Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. Gigascience 2014, 3:4.
    • (2014) Gigascience , vol.3 , pp. 4
    • Huntley, R.P.1    Sawford, T.2    Martin, M.J.3    O'Donovan, C.4
  • 26
    • 84933073669 scopus 로고    scopus 로고
    • Ubiquitylation, neddylation and the DNA damage response
    • Brown J.S., Jackson S.P. Ubiquitylation, neddylation and the DNA damage response. Open Biol. 2015, 5.
    • (2015) Open Biol. , vol.5
    • Brown, J.S.1    Jackson, S.P.2
  • 27
    • 0026763128 scopus 로고
    • Identification of a set of genes with developmentally down-regulated expression in the mouse brain
    • Kumar S., Tomooka Y., Noda M. Identification of a set of genes with developmentally down-regulated expression in the mouse brain. Biochem. Biophys. Res. Commun. 1992, 185:1155-1161.
    • (1992) Biochem. Biophys. Res. Commun. , vol.185 , pp. 1155-1161
    • Kumar, S.1    Tomooka, Y.2    Noda, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.