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Volumn 29, Issue 5, 2013, Pages 645-646

GKaKs: The pipeline for genome-level Ka/Ks calculation

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; CODON; COMPUTER PROGRAM; DNA SEQUENCE; FRAMESHIFT MUTATION; GENOMICS; HUMAN; METHODOLOGY; MOUSE; RAT; SEQUENCE ALIGNMENT; STOP CODON;

EID: 84874710448     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt009     Document Type: Article
Times cited : (35)

References (17)
  • 1
    • 77954272855 scopus 로고    scopus 로고
    • TranslatorX: Multiple alignment of nucleotide sequences guided by amino acid translations
    • Abascal, F. et al. (2010) TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res., 38, W7-W13.
    • (2010) Nucleic Acids Res. , vol.38
    • Abascal, F.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
    • 85046912995 scopus 로고    scopus 로고
    • A test for faster X evolution in Drosophila
    • Andrea, J. B. et al. (2002) A test for faster X evolution in Drosophila. Mol. Biol. Evol., 19, 1816-1819.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1816-1819
    • Andrea, J.B.1
  • 4
    • 25444472044 scopus 로고    scopus 로고
    • TransAlign: Using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
    • Bininda-Emonds, O. R. P. (2005) transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics, 6, 156.
    • (2005) BMC Bioinformatics , vol.6 , pp. 156
    • Bininda-Emonds, O.R.P.1
  • 5
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman, N. and Yang, Z. (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol., 11, 725-736.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 6
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • DOI 10.1101/gr.229202. Article published online before March 2002
    • Kent, W. J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664. (Pubitemid 34308645)
    • (2002) Genome Research , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 7
    • 67349173173 scopus 로고    scopus 로고
    • More radical amino acid replacements in primates than in rodents: Support for the evolutionary role of effective population size
    • Hughes, A. L. and Friedman, R. (2009) More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene, 440, 50-56.
    • (2009) Gene , vol.440 , pp. 50-56
    • Hughes, A.L.1    Friedman, R.2
  • 8
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • Li, W. H. et al. (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol., 2, 150-174. (Pubitemid 15239737)
    • (1985) Molecular Biology and Evolution , vol.2 , Issue.2 , pp. 150-174
    • Li, W.H.1    Wu, C.I.2    Luo, C.C.3
  • 9
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei, M. and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3, 418-426. (Pubitemid 16010523)
    • (1986) Molecular Biology and Evolution , vol.3 , Issue.5 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 10
    • 80052824121 scopus 로고    scopus 로고
    • MACSE: Multiple alignment of coding SEquences accounting for frameshifts and stop codons
    • Ranwez, V. et al. (2011) MACSE: multiple alignment of coding SEquences accounting for frameshifts and stop codons. PloS One, 6, e22594.
    • (2011) PloS One , vol.6
    • Ranwez, V.1
  • 12
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • DOI 10.1093/nar/gkl315
    • Suyama, M. et al. (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res., 34, W609-W612. (Pubitemid 44529842)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 13
    • 0043123111 scopus 로고    scopus 로고
    • RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
    • DOI 10.1093/nar/gkg609
    • Wernersson, R. and Pedersen, A. H. (2003) RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res., 31, 3537-3539. (Pubitemid 37442193)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3537-3539
    • Wernersson, R.1    Pedersen, A.G.2
  • 14
    • 77955375616 scopus 로고    scopus 로고
    • Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection
    • Wolf, J. B. W. et al. (2009) Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol. Evol., 1, 308-319.
    • (2009) Genome Biol. Evol. , vol.1 , pp. 308-319
    • Wolf, J.B.W.1
  • 15
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • DOI 10.1093/molbev/msm088
    • Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591. (Pubitemid 47236688)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1
  • 16
    • 79961064486 scopus 로고    scopus 로고
    • Factors that contribute to variation in evolutionary rate among Arabidopsis genes
    • Yang, L. and Gaut, B. (2011) Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol. Biol. Evol., 28, 2359-2369.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2359-2369
    • Yang, L.1    Gaut, B.2
  • 17
    • 34248669040 scopus 로고    scopus 로고
    • KaKs-Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
    • DOI 10.1016/S1672-0229(07)60007-2, PII S1672022907600072
    • Zhang, Z. et al. (2006) KaKs-Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics, 4, 259-263. (Pubitemid 46771391)
    • (2006) Genomics, Proteomics and Bioinformatics , vol.4 , Issue.4 , pp. 259-263
    • Zhang, Z.1    Li, J.2    Zhao, X.-Q.3    Wang, J.4    Wong, G.K.-S.5    Yu, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.