메뉴 건너뛰기




Volumn 31, Issue 10, 2015, Pages 1544-1552

PANNZER: High-throughput functional annotation of uncharacterized proteins in an error-prone environment

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84929622388     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu851     Document Type: Article
Times cited : (117)

References (33)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped blast and psi-blast: A new generation of protein database search programs
    • 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
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 0031690080 scopus 로고    scopus 로고
    • Automatic extraction of keywords from scientific text: Application to the knowledge domain of protein families
    • Andrade M.A. and Valencia A. (1998). Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics, 14, 600-607
    • (1998) Bioinformatics , vol.14 , pp. 600-607
    • Andrade, M.A.1    Valencia, A.2
  • 3
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner S.E. (1999). Errors in genome annotation. Trends Genet.: TIG, 15, 132-133
    • (1999) Trends Genet. TIG , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 4
    • 84878083062 scopus 로고    scopus 로고
    • Protein function prediction by massive integration of evolutionary analyses and multiple data sources
    • Cozzetto D., et al. (2013). Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics, 14(Suppl. 3), S1
    • (2013) BMC Bioinformatics , vol.14 , pp. S1
    • Cozzetto, D.1
  • 5
    • 84864928775 scopus 로고    scopus 로고
    • Argot2: A large scale function prediction tool relying on semantic similarity of weighted gene ontology terms
    • Falda M., et al. (2012). Argot2: a large scale function prediction tool relying on semantic similarity of weighted gene ontology terms. BMC Bioinformatics, 13(Suppl. 4), S14
    • (2012) BMC Bioinformatics , vol.13 , pp. S14
    • Falda, M.1
  • 6
    • 0035109680 scopus 로고    scopus 로고
    • Functional and structural genomics using pedant
    • Frishman D., et al. (2001). Functional and structural genomics using pedant. Bioinformatics, 17, 44-57
    • (2001) Bioinformatics , vol.17 , pp. 44-57
    • Frishman, D.1
  • 7
    • 12244283680 scopus 로고    scopus 로고
    • Modeling the percolation of annotation errors in a database of protein sequences
    • Gilks W.R., et al. (2002). Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics, 18, 1641-1649
    • (2002) Bioinformatics , vol.18 , pp. 1641-1649
    • Gilks, W.R.1
  • 8
    • 14644389482 scopus 로고    scopus 로고
    • Percolation of annotation errors through hierarchically structured protein sequence databases
    • Gilks W.R., et al. (2005). Percolation of annotation errors through hierarchically structured protein sequence databases. Math. Biosci., 193, 223-234
    • (2005) Math. Biosci , vol.193 , pp. 223-234
    • Gilks, W.R.1
  • 9
    • 45549089420 scopus 로고    scopus 로고
    • High-throughput functional annotation and data mining with the blast2go suite
    • Götz S., et al. (2008). High-throughput functional annotation and data mining with the blast2go suite. Nucleic Acids Res., 36, 3420-3435
    • (2008) Nucleic Acids Res , vol.36 , pp. 3420-3435
    • Götz, S.1
  • 10
    • 0142155182 scopus 로고    scopus 로고
    • Righting the wrongs
    • Hadley C. (2003). Righting the wrongs. EMBO Rep., 4, 829-831
    • (2003) Embo Rep , vol.4 , pp. 829-831
    • Hadley, C.1
  • 11
    • 34250790725 scopus 로고    scopus 로고
    • Estimating the annotation error rate of curated go database sequence annotations
    • Jones C.E., et al. (2007). Estimating the annotation error rate of curated go database sequence annotations. BMC Bioinformatics, 8, 170
    • (2007) BMC Bioinformatics , vol.8 , pp. 170
    • Jones, C.E.1
  • 12
    • 84857023557 scopus 로고    scopus 로고
    • Blannotator: Enhanced homology-based function prediction of bacterial proteins
    • Kankainen M., et al. (2012). Blannotator: enhanced homology-based function prediction of bacterial proteins. BMC Bioinformatics, 13, 33
    • (2012) BMC Bioinformatics , vol.13 , pp. 33
    • Kankainen, M.1
  • 13
    • 25444458848 scopus 로고    scopus 로고
    • Autofact: An automatic functional annotation and classification tool
    • Koski L.B., et al. (2005). Autofact: an automatic functional annotation and classification tool. BMC Bioinformatics, 6, 151
    • (2005) BMC Bioinformatics , vol.6 , pp. 151
    • Koski, L.B.1
  • 14
    • 84866458775 scopus 로고    scopus 로고
    • Sans: High-throughput retrieval of protein sequences allowing 50 mismatches
    • Koskinen J.P. and Holm L. (2012). Sans: high-throughput retrieval of protein sequences allowing 50 mismatches. Bioinformatics, 28, i438-i443
    • (2012) Bioinformatics , vol.28 , pp. i438-i443
    • Koskinen, J.P.1    Holm, L.2
  • 15
    • 0005180705 scopus 로고    scopus 로고
    • An information-theoretic definition of similarity
    • Lin D. (1998). An information-theoretic definition of similarity. In: International Conference on Machine Learning (ICML), Vol. 98, pp. 296-304
    • (1998) International Conference on Machine Learning (ICML , vol.98 , pp. 296-304
    • Lin, D.1
  • 16
    • 79960976768 scopus 로고    scopus 로고
    • UniProt knowledgebase: A hub of integrated protein data
    • Oxford bar009
    • Magrane M. and Consortium U. (2011). UniProt knowledgebase: a hub of integrated protein data. Database (Oxford), 2011, bar009
    • (2011) Database , vol.2011
    • Magrane, M.1    Consortium, U.2
  • 17
    • 13244268370 scopus 로고    scopus 로고
    • Gotcha: A new method for prediction of protein function assessed by the annotation of seven genomes
    • Martin D.M., et al. (2004). Gotcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics, 5, 178
    • (2004) BMC Bioinformatics , vol.5 , pp. 178
    • Martin, D.M.1
  • 18
    • 73349120997 scopus 로고    scopus 로고
    • Figfams: Yet another set of protein families
    • Meyer F., et al. (2009). Figfams: yet another set of protein families. Nucleic Acids Res., 37, 6643-6654
    • (2009) Nucleic Acids Res , vol.37 , pp. 6643-6654
    • Meyer, F.1
  • 20
    • 9144265895 scopus 로고    scopus 로고
    • Retrieving sequences of enzymes experimentally characterized but erroneously annotated: The case of the putrescine carbamoyltransferase
    • Naumoff D.G., et al. (2004). Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase. BMC Genomics, 5, 52
    • (2004) BMC Genomics , vol.5 , pp. 52
    • Naumoff, D.G.1
  • 21
    • 84891804612 scopus 로고    scopus 로고
    • The seed and the rapid annotation of microbial genomes using subsystems technology (rast
    • Overbeek R., et al. (2013). The seed and the rapid annotation of microbial genomes using subsystems technology (rast). Nucleic Acids Res., 42, D206-D214
    • (2013) Nucleic Acids Res , vol.42 , pp. D206-D214
    • Overbeek, R.1
  • 22
    • 68249087607 scopus 로고    scopus 로고
    • Semantic similarity in biomedical ontologies
    • Pesquita C., et al. (2009). Semantic similarity in biomedical ontologies. PLoS Comput. Biol., 5, e1000443
    • (2009) Plos Comput. Biol , vol.5 , pp. e1000443
    • Pesquita, C.1
  • 23
    • 55449125498 scopus 로고    scopus 로고
    • The rough guide to in silico function prediction or how to use sequence and structure information to predict protein function
    • Punta M. and Ofran Y. (2008). The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput. Biol., 4, e1000160
    • (2008) Plos Comput. Biol , vol.4 , pp. e1000160
    • Punta, M.1    Ofran, Y.2
  • 24
    • 84874663959 scopus 로고    scopus 로고
    • A large-scale evaluation of computational protein function prediction
    • Radivojac P., et al. (2013). A large-scale evaluation of computational protein function prediction. Nat. Methods, 10, 221-227
    • (2013) Nat. Methods , vol.10 , pp. 221-227
    • Radivojac, P.1
  • 25
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Robert T. (1996). Regression shrinkage and selection via the lasso. J. R. Stat. Soc., 58, 267-288
    • (1996) J. R. Stat. Soc , vol.58 , pp. 267-288
    • Robert, T.1
  • 27
  • 28
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on gene ontology
    • Schlicker A., et al. (2006). A new measure for functional similarity of gene products based on gene ontology. BMC Bioinformatics, 7, 302
    • (2006) BMC Bioinformatics , vol.7 , pp. 302
    • Schlicker, A.1
  • 29
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
    • Schnoes A.M., et al. (2009). Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605
    • (2009) Plos Comput. Biol , vol.5 , pp. e1000605
    • Schnoes, A.M.1
  • 30
    • 84878483493 scopus 로고    scopus 로고
    • Biases in the experimental annotations of protein function and their effect on our understanding of protein function space
    • Schnoes A.M., et al. (2013). Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput. Biol., 9, e1003063
    • (2013) Plos Comput. Biol , vol.9 , pp. e1003063
    • Schnoes, A.M.1
  • 31
    • 70449392630 scopus 로고    scopus 로고
    • Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
    • Toronen P., et al. (2009). Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinformatics, 10, 307
    • (2009) BMC Bioinformatics , vol.10 , pp. 307
    • Toronen, P.1
  • 32
    • 13244299124 scopus 로고    scopus 로고
    • Applying support vector machines for gene ontology based gene function prediction
    • Vinayagam A., et al. (2004). Applying support vector machines for gene ontology based gene function prediction. BMC Bioinformatics, 5, 116
    • (2004) BMC Bioinformatics , vol.5 , pp. 116
    • Vinayagam, A.1
  • 33
    • 13444282007 scopus 로고    scopus 로고
    • Filtering erroneous protein annotation
    • Wieser D., et al. (2004). Filtering erroneous protein annotation. Bioinformatics, 20(Suppl. 1), i342-i347
    • (2004) Bioinformatics , vol.20 , pp. i342-i347
    • Wieser, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.