메뉴 건너뛰기




Volumn 29, Issue 8, 2013, Pages 989-995

Making automated multiple alignments of very large numbers of protein sequences

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; METHODOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 84876220535     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt093     Document Type: Article
Times cited : (46)

References (37)
  • 1
    • 0023571979 scopus 로고
    • Evaluation and improvements in the auto- matic alignment of protein sequences
    • Barton, GJ. and Sternberg, MJ. (1987) Evaluation and improvements in the auto- matic alignment of protein sequences. Protein Eng., 1, 89-94.
    • (1987) Protein Eng. , vol.1 , pp. 89-94
    • Barton, G.J.1    Sternberg, M.J.2
  • 2
    • 79960414804 scopus 로고    scopus 로고
    • Aligning short reads to reference alignments and trees
    • Berger, S.A. and 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
  • 3
    • 77952039847 scopus 로고    scopus 로고
    • Sequence emBedding for fast construction of guide trees for multiple sequence alignment
    • Blackshields, G. et al. (2010) Sequence emBedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol. Biol., 5, 21.
    • (2010) Algorithms Mol. Biol. , vol.5 , pp. 21
    • Blackshields, G.1
  • 4
    • 67049158348 scopus 로고    scopus 로고
    • Fast statistical alignment
    • Bradley, R.K. et al. (2009) Fast statistical alignment. PLoS Comput. Biol., 5, e1000392.
    • (2009) PLoS Comput. Biol. , vol.5
    • Bradley, R.K.1
  • 5
    • 84867781208 scopus 로고    scopus 로고
    • Epistasis as the primary factor in molecular evolution
    • Breen, M.S. et al. (2012) Epistasis as the primary factor in molecular evolution. Nature, 490, 535-538.
    • (2012) Nature , vol.490 , pp. 535-538
    • Breen, M.S.1
  • 6
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do, C.B. et al. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
    • (2005) Genome Res. , vol.15 , pp. 330-340
    • Do, C.B.1
  • 7
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 8
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders ofmagnitude faster than BLAST
    • Edgar, R.C. (2010) Search and clustering orders ofmagnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 9
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: Interactive sequence similarity searching
    • Finn, R.D. et al. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39 (Suppl. 2), W29-W37.
    • (2011) Nucleic Acids Res. , vol.39 , Issue.SUPPL. 2
    • Finn, R.D.1
  • 10
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence align- ment based on fast Fourier transform
    • Katoh, K. et al. (2002) MAFFT: a novel method for rapid multiple sequence align- ment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1
  • 11
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K. et al. (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
  • 12
    • 33847310423 scopus 로고    scopus 로고
    • PartTree: An algorithm to build an approximate tree from a large number ofunaligned sequences
    • Katoh, K. and Toh, H. (2007) PartTree: an algorithm to build an approximate tree from a large number ofunaligned sequences. Bioinformatics, 23, 372-374.
    • (2007) Bioinformatics , vol.23 , pp. 372-374
    • Katoh, K.1    Toh, H.2
  • 13
    • 84870466552 scopus 로고    scopus 로고
    • Adding unaligned sequences into an existing align- ment using MAFFT and LAST
    • Katoh, K. and Frith, M.C. (2012) Adding unaligned sequences into an existing align- ment using MAFFT and LAST. Bioinformatics, 28, 3144-3146.
    • (2012) Bioinformatics , vol.28 , pp. 3144-3146
    • Katoh, K.1    Frith, M.C.2
  • 14
    • 70349866695 scopus 로고    scopus 로고
    • Upcoming challenges for multiple sequence alignment methods in the high-throughput era
    • Kemena, C. and Notredame, C. (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
    • (2009) Bioinformatics , vol.25 , pp. 2455-2465
    • Kemena, C.1    Notredame, C.2
  • 15
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin, M.A. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 16
    • 29244447181 scopus 로고    scopus 로고
    • Kalign-an accurate and fast multiple sequence alignment algorithm
    • Lassmann, T. and Sonnhammer, E.L (2005) Kalign-an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics, 6, 298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 298
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 17
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Lee, C. et al. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics, 18, 452-464.
    • (2002) Bioinformatics , vol.18 , pp. 452-464
    • Lee, C.1
  • 18
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 19
    • 67649240664 scopus 로고    scopus 로고
    • Rapid and accurate large-scale coestimation of sequence align- ments and phylogenetic trees
    • Liu, K. et al. (2009) Rapid and accurate large-scale coestimation of sequence align- ments and phylogenetic trees. Science, 324, 1561-1564.
    • (2009) Science , vol.324 , pp. 1561-1564
    • Liu, K.1
  • 20
    • 77955352019 scopus 로고    scopus 로고
    • MSAProbs: Multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
    • Liu, Y. et al. (2010) MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics, 26, 1958-1964.
    • (2010) Bioinformatics , vol.26 , pp. 1958-1964
    • Liu, Y.1
  • 21
    • 46249095233 scopus 로고    scopus 로고
    • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    • Loytynoja, A. and Goldman, N. (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320, 1632-1635.
    • (2008) Science , vol.320 , pp. 1632-1635
    • Loytynoja, A.1    Goldman, N.2
  • 22
    • 84864006216 scopus 로고    scopus 로고
    • Accurate extension ofmultiple sequence alignments using a phylogeny-aware graph algorithm
    • Loytynoja, A. et al. (2012) Accurate extension ofmultiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics, 28, 1684-1691.
    • (2012) Bioinformatics , vol.28 , pp. 1684-1691
    • Loytynoja, A.1
  • 23
    • 82855163967 scopus 로고    scopus 로고
    • Protein 3D structure computed from evolutionary sequence variation
    • Marks, D.S. et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One, 6, e28766.
    • (2011) PLoS One , vol.6
    • Marks, D.S.1
  • 24
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure align- ments for homologous families
    • Mizuguchi, K. et al. (2008) HOMSTRAD: a database of protein structure align- ments for homologous families. Protein Sci., 7, 2469-2471.
    • (2008) Protein Sci. , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1
  • 25
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple se- quence alignment
    • Morgenstern, B. et al. (1998) DIALIGN: finding local similarities by multiple se- quence alignment. Bioinformatics, 14, 290-294.
    • (1998) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1
  • 26
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C. et al. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-218.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-218
    • Notredame, C.1
  • 27
    • 33750001271 scopus 로고    scopus 로고
    • MUMMALS: Multiple sequence alignment im- proved by using hidden Markov models with local structural information
    • Pei, J. and Grishin, N.V. (2006) MUMMALS: multiple sequence alignment im- proved by using hidden Markov models with local structural information. Nucleic Acids Res., 34, 4364-4374.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4364-4374
    • Pei, J.1    Grishin, N.V.2
  • 28
    • 34248532415 scopus 로고    scopus 로고
    • PROMALS: Towards accurate multiple sequence alignments of distantly related proteins
    • Pei, J. and Grishin, N.V. (2007) PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.
    • (2007) Bioinformatics , vol.23 , pp. 802-808
    • Pei, J.1    Grishin, N.V.2
  • 29
    • 84858077472 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Punta, M. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
    • (2012) Nucleic Acids Res. , vol.40
    • Punta, M.1
  • 30
    • 33751004142 scopus 로고    scopus 로고
    • Probalign: Multiple sequence alignment using partition function posterior probabilities
    • Roshan, U. and Livesay, D.R. (2006) Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics, 22, 2715-2721.
    • (2006) Bioinformatics , vol.22 , pp. 2715-2721
    • Roshan, U.1    Livesay, D.R.2
  • 31
    • 78650845114 scopus 로고    scopus 로고
    • A complete analysis of HA and NA genes of influenza A viruses
    • Shi, W. et al. (2010) A complete analysis of HA and NA genes of influenza A viruses. PLoS One, 5, e14454.
    • (2010) PLoS One , vol.5
    • Shi, W.1
  • 32
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • Sievers, F. et al. (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
  • 33
    • 33645985806 scopus 로고    scopus 로고
    • A polynomial time solvable formulation ofmultiple sequence alignment
    • Sze, S.H. et al. (2006) A polynomial time solvable formulation ofmultiple sequence alignment. J. Comput. Biol., 13, 309-319.
    • (2006) J. Comput. Biol. , vol.13 , pp. 309-319
    • Sze, S.H.1
  • 34
    • 23144440940 scopus 로고    scopus 로고
    • PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure informa- tion
    • Simossis, V.A. and Heringa, J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure informa- tion. Nucleic Acids Res., 33 (Suppl. 2), W289-W294.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.SUPPL. 2
    • Simossis, V.A.1    Heringa, J.2
  • 35
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
    • Thompson, J.D. et al. (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
    • (2005) Proteins , vol.61 , pp. 127-136
    • Thompson, J.D.1
  • 36
    • 79953307693 scopus 로고    scopus 로고
    • A comprehensive benchmark study ofmultiple se- quence alignment methods: Current challenges and future perspectives
    • Thompson, J.D. et al. (2011) A comprehensive benchmark study ofmultiple se- quence alignment methods: current challenges and future perspectives. PloS One, 6, e18093.
    • (2011) PloS One , vol.6
    • Thompson, J.D.1
  • 37
    • 34547840223 scopus 로고    scopus 로고
    • Multiple alignment by aligning alignments
    • Wheeler, T.J. and Kececioglu, J.D. (2007) Multiple alignment by aligning alignments. Bioinformatics, 23, i559-i568.
    • (2007) Bioinformatics , vol.23
    • Wheeler, T.J.1    Kececioglu, J.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.