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PMID: 17784778 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Recent evolutions of multiple sequence alignment algorithms.

PLoS computational biology ·Vol. 3 ·No. 8 ·2007-08-00 ·Pages e123

Notredame C

Abstract

暂无摘要

MeSH Terms
Algorithms Base Sequence Chromosome Mapping/methods,trends Molecular Sequence Data Sequence Alignment/methods,trends Sequence Analysis, DNA/methods,trends
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Notredame Cédric
Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, Marseille, France. [email protected]
References (32)
32 references, click to expand
  1. Protein structure comparison using iterated double dynamic programming.
    Protein Sci. 1999 Mar;8(3):654-65 PMID: 10091668
  2. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
    J Mol Biol. 2001 Jun 29;310(1):243-57 PMID: 11419950
  3. Analysis and comparison of benchmarks for multiple sequence alignment.
    In Silico Biol. 2006;6(4):321-39 PMID: 16922695
  4. The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.
    Bioinformatics. 2002 Sep;18(9):1243-9 PMID: 12217916
  5. PCMA: fast and accurate multiple sequence alignment based on profile consistency.
    Bioinformatics. 2003 Feb 12;19(3):427-8 PMID: 12584134
  6. APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.
    Bioinformatics. 2003;19 Suppl 1:i215-21 PMID: 12855461
  7. 3DCoffee: combining protein sequences and structures within multiple sequence alignments.
    J Mol Biol. 2004 Jul 2;340(2):385-95 PMID: 15201059
  8. CaspR: a web server for automated molecular replacement using homology modelling.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9 PMID: 15215460
  9. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics. 2004 Aug 19;5:113 PMID: 15318951
  10. The alignment of sets of sequences and the construction of phyletic trees: an integrated method.
    J Mol Evol. 1984;20(2):175-86 PMID: 6433036
  11. Identification of protein sequence homology by consensus template alignment.
    J Mol Biol. 1986 Mar 20;188(2):233-58 PMID: 3088284
  12. Protein structure alignment.
    J Mol Biol. 1989 Jul 5;208(1):1-22 PMID: 2769748
  13. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
  14. Multiple DNA and protein sequence alignment based on segment-to-segment comparison.
    Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12098-103 PMID: 8901539
  15. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information.
    Nucleic Acids Res. 2006;34(16):4364-74 PMID: 16936316
  16. MAFFT version 5: improvement in accuracy of multiple sequence alignment.
    Nucleic Acids Res. 2005;33(2):511-8 PMID: 15661851
  17. PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
    Bioinformatics. 2007 Apr 1;23(7):802-8 PMID: 17267437
  18. ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res. 2005 Feb;15(2):330-40 PMID: 15687296
  19. Multiple sequence alignments.
    Curr Opin Struct Biol. 2005 Jun;15(3):261-6 PMID: 15963889
  20. PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94 PMID: 15980472
  21. SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
    Bioinformatics. 2005 Sep 15;21(18):3615-21 PMID: 16020471
  22. Automatic assessment of alignment quality.
    Nucleic Acids Res. 2005;33(22):7120-8 PMID: 16361270
  23. Kalign--an accurate and fast multiple sequence alignment algorithm.
    BMC Bioinformatics. 2005;6:298 PMID: 16343337
  24. M-Coffee: combining multiple sequence alignment methods with T-Coffee.
    Nucleic Acids Res. 2006;34(6):1692-9 PMID: 16556910
  25. Multiple sequence alignment.
    Curr Opin Struct Biol. 2006 Jun;16(3):368-73 PMID: 16679011
  26. Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W596-9 PMID: 16845078
  27. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8 PMID: 16845081
  28. The iRMSD: a local measure of sequence alignment accuracy using structural information.
    Bioinformatics. 2006 Jul 15;22(14):e35-9 PMID: 16873492
  29. DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.
    Nucleic Acids Res. 2000 Aug 1;28(15):2919-26 PMID: 10908355
  30. T-Coffee: A novel method for fast and accurate multiple sequence alignment.
    J Mol Biol. 2000 Sep 8;302(1):205-17 PMID: 10964570
  31. ProSup: a refined tool for protein structure alignment.
    Protein Eng. 2000 Nov;13(11):745-52 PMID: 11161105
  32. Multiple sequence alignment: algorithms and applications.
    Adv Biophys. 1999;36:159-206 PMID: 10463075
Article Info
Journal
PLoS computational biology
Abbr.
PLoS Comput Biol
ISSN
1553-7358
DOI
10.1371/journal.pcbi.0030123
Email
[email protected]
Published
2007-08-00
Pages
e123
Language
English
Region
United States
NLM ID
101238922
PMCID
PMC1963500
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pcbi.0030123 PMC Full Text View journal details
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