메뉴 건너뛰기




Volumn 24, Issue 3, 2008, Pages 319-324

Choosing BLAST options for better detection of orthologs as reciprocal best hits

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN;

EID: 38849135019     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm585     Document Type: Article
Times cited : (372)

References (30)
  • 1
    • 33747892409 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and inparalogs shared-by mutiple proteomes
    • Alexeyenko,A. et al. (2006) Automatic clustering of orthologs and inparalogs shared-by mutiple proteomes. Bioinformatics, 22, e9-e15.
    • (2006) Bioinformatics , vol.22
    • Alexeyenko, A.1
  • 2
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 3
    • 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
  • 4
    • 0035875343 scopus 로고    scopus 로고
    • GeneMarkS: A self-training method for prediction of gone starts in microbial genomes implications for finding sequence motifs in regulatory regions
    • Besemer,J. et al. (2001) GeneMarkS: A self-training method for prediction of gone starts in microbial genomes implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29 2607-2618.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2607-2618
    • Besemer, J.1
  • 5
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner,F.R. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
    • (1997) Science , vol.277 , pp. 1453-1474
    • Blattner, F.R.1
  • 6
    • 0037255072 scopus 로고    scopus 로고
    • The SWISS-PROT protein knowledgebase and its supplement TrEMBE in 2003
    • Boeckmann,B. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBE in 2003. Nucleic Acids Res., 31, 365-370.
    • (2003) Nucleic Acids Res , vol.31 , pp. 365-370
    • Boeckmann, B.1
  • 7
    • 0032491377 scopus 로고    scopus 로고
    • Predicting function: From genes to genomes and back
    • Bork,P. et al. (1998) Predicting function: From genes to genomes and back. J. Mol. Biol., 283, 707-725.
    • (1998) J. Mol. Biol , vol.283 , pp. 707-725
    • Bork, P.1
  • 8
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner,S.E. et al. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA, 95, 6073-6078.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1
  • 9
    • 33747817416 scopus 로고    scopus 로고
    • Roundup: A multi-genome repository of orthologs and evolutionary distances
    • Deluca,T.F. et al. (2006) Roundup: A multi-genome repository of orthologs and evolutionary distances. Bioinformatics, 22, 2044-2046.
    • (2006) Bioinformatics , vol.22 , pp. 2044-2046
    • Deluca, T.F.1
  • 10
    • 3042739661 scopus 로고    scopus 로고
    • What is dynamic programming?
    • Eddy,S.R. (2004) What is dynamic programming? Nat. biotechnol., 22, 909-910.
    • (2004) Nat. biotechnol , vol.22 , pp. 909-910
    • Eddy, S.R.1
  • 11
    • 0034178257 scopus 로고    scopus 로고
    • Homology a personal view on some of the problems
    • Fitch,W.M. (2000) Homology a personal view on some of the problems. Trends Genet., 16, 227-231.
    • (2000) Trends Genet , vol.16 , pp. 227-231
    • Fitch, W.M.1
  • 12
    • 20044369186 scopus 로고    scopus 로고
    • An adaptive radiation model for the origin of new gene functions
    • Francino,M.P. (2005) An adaptive radiation model for the origin of new gene functions. Nat. Genet., 37, 573-577.
    • (2005) Nat. Genet , vol.37 , pp. 573-577
    • Francino, M.P.1
  • 13
    • 33746755926 scopus 로고    scopus 로고
    • Improving the specificity of high-throughput ortholog prediction
    • Fulton,D.L. et al. (2006) Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics, 7, 270.
    • (2006) BMC Bioinformatics , vol.7 , pp. 270
    • Fulton, D.L.1
  • 14
    • 0042423439 scopus 로고    scopus 로고
    • Automated annotation of microbial proteomes in SWISS-PROT
    • Gattiker,A. et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem., 27, 49-58.
    • (2003) Comput. Biol. Chem , vol.27 , pp. 49-58
    • Gattiker, A.1
  • 15
    • 6044261571 scopus 로고    scopus 로고
    • Conservation of adjacency as evidence of paralogous operons
    • Janga,S.C. and Moreno-Hagelsieb,G. (2004) Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res., 32, 5392-5397.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5392-5397
    • Janga, S.C.1    Moreno-Hagelsieb, G.2
  • 16
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski,L.B. and Golding,G.B. (2001) The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol., 52, 540-542.
    • (2001) J. Mol. Evol , vol.52 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 17
    • 0033965854 scopus 로고    scopus 로고
    • NCBI's LocusLink and RefSeq
    • Maglott,D.R. et al. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res., 28, 126-128.
    • (2000) Nucleic Acids Res , vol.28 , pp. 126-128
    • Maglott, D.R.1
  • 18
    • 0001291140 scopus 로고    scopus 로고
    • A powerful non-homology method for the prediction of operons in prokaryotes
    • Moreno-Hagelsieb,G. and Collado-Vides,J. (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 (Suppl. 1), S329-S336.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Moreno-Hagelsieb, G.1    Collado-Vides, J.2
  • 20
    • 0034764340 scopus 로고    scopus 로고
    • Having a BLAST with bioinformatics (and avoiding BLASTphenry)
    • REVIEWS2002
    • Pertsemlidis,A. and Fondon,J.W.3rd (2001) Having a BLAST with bioinformatics (and avoiding BLASTphenry). Genome Biol., 2 REVIEWS2002.
    • (2001) Genome Biol , vol.2
    • Pertsemlidis, A.1    Fondon 3rd, J.W.2
  • 21
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Database Issue, D501-D504
    • Pruitt,K.D. et al. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33 (Database Issue), D501-D504.
    • (2005) Nucleic Acids Res , vol.33
    • Pruitt, K.D.1
  • 22
    • 0035878724 scopus 로고    scopus 로고
    • Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    • Schaffer,A.A. et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2994-3005
    • Schaffer, A.A.1
  • 23
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 24
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov,R.L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1
  • 25
    • 0042902833 scopus 로고    scopus 로고
    • The cog database: An update version includes eukaryotes
    • Tatusov,R.L. et al. (2003) The cog database: An update version includes eukaryotes. BMC Bioinformatics, 4, 41.
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 26
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1
  • 27
    • 33846086800 scopus 로고    scopus 로고
    • recent developments in the integration and prediction of protein interactions
    • Database issue, D358-D362, STRING 7
    • von Mering,C. et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res., 35 (Database issue), D358-D362.
    • (2007) Nucleic Acids Res , vol.35
    • von Mering, C.1
  • 28
    • 0141626909 scopus 로고
    • (1003) Detecting putative orthologs
    • Wall,D.P. et al. (1003) Detecting putative orthologs. Bioinformatics, 19, 1710-1711.
    • (1710) Bioinformatics , vol.19
    • Wall, D.P.1
  • 29
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenac analysis by maximum likelihood
    • Yang,Z. (1997) PAML: A program package for phylogenac analysis by maximum likelihood. Comput. Appl. Biosci., 13, 555-556.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 30
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang,Z. (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591.
    • (2007) Mol. Biol. Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.