메뉴 건너뛰기




Volumn 30, Issue 4, 2013, Pages 772-780

MAFFT multiple sequence alignment software version 7: Improvements in performance and usability

Author keywords

metagemone; multiple sequence alignment; parallel processing; progressive alignment; protein structure

Indexed keywords

INTERNAL TRANSCRIBED SPACER;

EID: 84875619226     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst010     Document Type: Article
Times cited : (29838)

References (48)
  • 1
    • 0032126517 scopus 로고    scopus 로고
    • Generalized affine gap costs for protein sequence alignment
    • Altschul SF. 1998. Generalized affine gap costs for protein sequence alignment. Proteins 32:88-96..
    • (1998) Proteins , vol.32 , pp. 88-96
    • Altschul, S.F.1
  • 2
    • 0023518540 scopus 로고
    • A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons
    • Barton GJ, Sternberg MJ. 1987. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol. 198:327-337..
    • (1987) J Mol Biol. , vol.198 , pp. 327-337
    • Barton, G.J.1    Sternberg, M.J.2
  • 3
    • 0026009526 scopus 로고
    • A novel randomized iterative strategy for aligning multiple protein sequences
    • Berger MP, Munson PJ. 1991. A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci. 7:479-484..
    • (1991) Comput Appl Biosci. , vol.7 , pp. 479-484
    • Berger, M.P.1    Munson, P.J.2
  • 4
    • 79960414804 scopus 로고    scopus 로고
    • Aligning short reads to reference alignments and trees
    • Berger SA, Stamatakis A. 2011. Aligning short reads to reference alignments and trees. Bioinformatics 27:2068-2075..
    • (2011) Bioinformatics , vol.27 , pp. 2068-2075
    • Berger, S.A.1    Stamatakis, A.2
  • 5
    • 84873584506 scopus 로고    scopus 로고
    • Class of multiple sequence alignment algorithm affects genomic analysis
    • access published December 4, 2012 doi:10.1093/molbev/mss256
    • Blackburne BP, Whelan S. 2012a. Class of multiple sequence alignment algorithm affects genomic analysis. Mol Biol Evol. Advance access published December 4, 2012, doi:10.1093/molbev/mss256
    • (2012) Mol Biol Evol. Advance
    • Blackburne, B.P.1    Whelan, S.2
  • 6
    • 84857171783 scopus 로고    scopus 로고
    • Measuring the distance between multiple sequence alignments
    • Blackburne BP, Whelan S. 2012b. Measuring the distance between multiple sequence alignments. Bioinformatics 28:495-502..
    • (2012) Bioinformatics , vol.28 , pp. 495-502
    • Blackburne, B.P.1    Whelan, S.2
  • 7
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • 14 Co-authors
    • Cannone JJ, Subramanian S, Schnare MN, et al. (14 co-authors). 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3:2..
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.J.1    Subramanian, S.2    Schnare, M.N.3
  • 8
    • 58149200948 scopus 로고    scopus 로고
    • The ribosomal database project: Improved alignments and new tools for rRNA analysis
    • 11 Co-authors
    • Cole JR,Wang Q, Cardenas E, et al. (11 co-authors). 2009. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145..
    • (2009) Nucleic Acids Res. , vol.37
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3
  • 9
    • 77950538424 scopus 로고    scopus 로고
    • Phylogenetic assessment of alignments reveals neglected tree signal in gaps
    • Dessimoz C, Gil M. 2010. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol. 11:R37..
    • (2010) Genome Biol. , vol.11
    • Dessimoz, C.1    Gil, M.2
  • 10
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng DF, Doolittle RF. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 25:351-360..
    • (1987) J Mol Evol. , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 11
    • 67749108209 scopus 로고    scopus 로고
    • INDELible: A flexible simulator of biological sequence evolution
    • Fletcher W, Yang Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol. 26:1879-1888..
    • (2009) Mol Biol Evol. , vol.26 , pp. 1879-1888
    • Fletcher, W.1    Yang, Z.2
  • 12
    • 35848948397 scopus 로고    scopus 로고
    • Mind the gaps: Evidence of bias in estimates of multiple sequence alignments
    • Golubchik T, Wise MJ, Easteal S, Jermiin LS. 2007. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. Mol Biol Evol. 24:2433-2442..
    • (2007) Mol Biol Evol. , vol.24 , pp. 2433-2442
    • Golubchik, T.1    Wise, M.J.2    Easteal, S.3    Jermiin, L.S.4
  • 13
    • 0027210418 scopus 로고
    • Optimal alignment between groups of sequences and its application to multiple sequence alignment
    • Gotoh O. 1993. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci. 9:361-370..
    • (1993) Comput Appl Biosci. , vol.9 , pp. 361-370
    • Gotoh, O.1
  • 14
    • 0028787980 scopus 로고
    • A weighting system and algorithm for aligning many phylogenetically related sequences
    • Gotoh O. 1995. A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci. 11:543-551..
    • (1995) Comput Appl Biosci. , vol.11 , pp. 543-551
    • Gotoh, O.1
  • 15
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 89:10915-10919..
    • (1992) Proc Natl Acad Sci U S A. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 16
    • 0024234855 scopus 로고
    • CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
    • Higgins DG, Sharp PM. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244..
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 17
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8: 275-282..
    • (1992) Comput Appl Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 18
    • 0028153788 scopus 로고
    • A mutation data matrix for transmembrane proteins
    • Jones DT, Taylor WR, Thornton JM. 1994. A mutation data matrix for transmembrane proteins. FEBS Lett. 339:269-275..
    • (1994) FEBS Lett. , vol.339 , pp. 269-275
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 19
    • 68049142320 scopus 로고    scopus 로고
    • Multiple alignment of DNA sequences with MAFFT
    • Katoh K, Asimenos G, Toh H. 2009. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol. 537:39-64..
    • (2009) Methods Mol Biol. , vol.537 , pp. 39-64
    • Katoh, K.1    Asimenos, G.2    Toh, H.3
  • 20
    • 84870466552 scopus 로고    scopus 로고
    • Adding unaligned sequences into an existing alignment using MAFFT and LAST
    • Katoh K, Frith MC. 2012. Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics 28:3144-3146..
    • (2012) Bioinformatics , vol.28 , pp. 3144-3146
    • Katoh, K.1    Frith, M.C.2
  • 21
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518..
    • (2005) Nucleic Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 22
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066..
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 23
    • 84887021829 scopus 로고    scopus 로고
    • Forthcoming 2013. MAFFT: Iterative refinement and additional methods
    • Katoh K, Standley DM. Forthcoming 2013. MAFFT: iterative refinement and additional methods. Methods Mol Biol.
    • Methods Mol Biol.
    • Katoh, K.1    Standley, D.M.2
  • 24
    • 33847310423 scopus 로고    scopus 로고
    • PartTree: An algorithm to build an approximate tree from a large number of unaligned sequences
    • Katoh K, Toh H. 2007. PartTree: An algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23: 372-374..
    • (2007) Bioinformatics , vol.23 , pp. 372-374
    • Katoh, K.1    Toh, H.2
  • 25
    • 44149125756 scopus 로고    scopus 로고
    • Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
    • Katoh K, Toh H. 2008a. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9:212..
    • (2008) BMC Bioinformatics , vol.9 , pp. 212
    • Katoh, K.1    Toh, H.2
  • 26
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh K, Toh H. 2008b. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298..
    • (2008) Brief Bioinform. , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 27
    • 77955019084 scopus 로고    scopus 로고
    • Parallelization of the MAFFT multiple sequence alignment program
    • Katoh K, Toh H. 2010. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26:1899-1900..
    • (2010) Bioinformatics , vol.26 , pp. 1899-1900
    • Katoh, K.1    Toh, H.2
  • 29
    • 77958119109 scopus 로고    scopus 로고
    • The impact of rRNA secondary structure consideration in alignment and tree reconstruction: Simulated data and a case study on the phylogeny of hexapods
    • Letsch HO, Kuck P, Stocsits RR, Misof B. 2010. The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. Mol Biol Evol. 27:2507-2521..
    • (2010) Mol Biol Evol. , vol.27 , pp. 2507-2521
    • Letsch, H.O.1    Kuck, P.2    Stocsits, R.R.3    Misof, B.4
  • 30
    • 84864006216 scopus 로고    scopus 로고
    • Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
    • Löytynoja A, Vilella AJ, Goldman N. 2012. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28:1684-1691..
    • (2012) Bioinformatics , vol.28 , pp. 1684-1691
    • Löytynoja, A.1    Vilella, A.J.2    Goldman, N.3
  • 31
    • 77958610660 scopus 로고    scopus 로고
    • Pplacer: Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen FA, Kodner RB, Armbrust EV. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11:538..
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.V.3
  • 32
    • 84864010118 scopus 로고    scopus 로고
    • SEPP: SATé-enabled phylogenetic placement
    • Mirarab S, Nguyen N, Warnow T. 2012. SEPP: SATé-enabled phylogenetic placement. Pac Symp Biocomput. 17:247-258..
    • (2012) Pac Symp Biocomput. , Issue.17 , pp. 247-258
    • Mirarab, S.1    Nguyen, N.2    Warnow, T.3
  • 34
    • 0031829993 scopus 로고    scopus 로고
    • COFFEE: An objective function for multiple sequence alignments
    • Notredame C, Holm L, Higgins DG. 1998. COFFEE: an objective function for multiple sequence alignments. Bioinformatics 14:407-422..
    • (1998) Bioinformatics , vol.14 , pp. 407-422
    • Notredame, C.1    Holm, L.2    Higgins, D.G.3
  • 35
    • 33750736013 scopus 로고    scopus 로고
    • The accuracy of several multiple sequence alignment programs for proteins
    • Nuin PA, Wang Z, Tillier ER. 2006. The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7:471..
    • (2006) BMC Bioinformatics , vol.7 , pp. 471
    • Nuin, P.A.1    Wang, Z.2    Tillier, E.R.3
  • 36
    • 2942619012 scopus 로고    scopus 로고
    • 3DCoffee: Combining protein sequences and structures within multiple sequence alignments
    • O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. 2004. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 340:385-395..
    • (2004) J Mol Biol. , vol.340 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 37
    • 42449090264 scopus 로고    scopus 로고
    • PROMALS3D: A tool for multiple protein sequence and structure alignments
    • Pei J, Kim BH, Grishin NV. 2008. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res. 36: 2295-2300..
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2295-2300
    • Pei, J.1    Kim, B.H.2    Grishin, N.V.3
  • 39
    • 79951529676 scopus 로고    scopus 로고
    • PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach
    • Sahraeian SM, Yoon BJ. 2011. PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinformatics 12:S38..
    • (2011) BMC Bioinformatics , vol.12
    • Sahraeian, S.M.1    Yoon, B.J.2
  • 41
    • 80054078476 scopus 로고    scopus 로고
    • Fast scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • 12 co-authors
    • Sievers F, Wilm A, Dineen D, et al. (12 co-authors). 2011. Fast scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 7:539..
    • (2011) Mol Syst Biol. , vol.7 , pp. 539
    • Sievers, F.1    Wilm, A.2    Dineen, D.3
  • 43
    • 34248201703 scopus 로고    scopus 로고
    • Ash structure alignment package: Sensitivity and selectivity in domain classification
    • Standley D, Toh H, Nakamura H. 2007. Ash structure alignment package: sensitivity and selectivity in domain classification. BMC Bioinformatics 8:116..
    • (2007) BMC Bioinformatics , vol.8 , pp. 116
    • Standley, D.1    Toh, H.2    Nakamura, H.3
  • 44
    • 4544295055 scopus 로고    scopus 로고
    • Detecting local structural similarity in proteins by maximizing number of equivalent residues
    • Standley DM, Toh H, Nakamura H. 2004. Detecting local structural similarity in proteins by maximizing number of equivalent residues. Proteins 57:381-391..
    • (2004) Proteins , vol.57 , pp. 381-391
    • Standley, D.M.1    Toh, H.2    Nakamura, H.3
  • 45
    • 84861143200 scopus 로고    scopus 로고
    • PhyLAT: A phylogenetic local alignment tool
    • Sun H, Buhler JD. 2012. PhyLAT: a phylogenetic local alignment tool. Bioinformatics 28:1336-1344..
    • (2012) Bioinformatics , vol.28 , pp. 1336-1344
    • Sun, H.1    Buhler, J.D.2
  • 46
    • 41749122381 scopus 로고    scopus 로고
    • A fast structuralmultiple alignment method for long RNA sequences
    • Tabei Y, Kiryu H, Kin T, Asai K. 2008. A fast structuralmultiple alignment method for long RNA sequences. BMC Bioinformatics 9:33..
    • (2008) BMC Bioinformatics , vol.9 , pp. 33
    • Tabei, Y.1    Kiryu, H.2    Kin, T.3    Asai, K.4
  • 47
    • 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 JD, Higgins DG, Gibson TJ. 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    Higgins, D.G.2    Gibson, T.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.