Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Molecular Systems Biology

Volumn 7, Issue , 2011, Pages

  Sievers, Fabian ^a   Wilm, Andreas ^b   Dineen, David ^a   Gibson, Toby J ^c   Karplus, Kevin ^d   Li, Weizhong ^e   Lopez, Rodrigo ^e   McWilliam, Hamish ^e   Remmert, Michael ^f   Söding, Johannes ^f   Thompson, Julie D ^g   Higgins, Desmond G ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d University of California Santa Cruz   (United States)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f UNIVERSITY OF MUNICH   (Germany)

^g UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

bioinformatics; hidden Markov models; multiple sequence alignment

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DATA BASE; HIDDEN MARKOV MODEL; MULTIPLE SEQUENCE ALIGNMENT; PRIORITY JOURNAL; SCORING SYSTEM; CHEMISTRY; DATA MINING; FACTUAL DATABASE; INSTRUMENTATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SYSTEMS BIOLOGY;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; BASE SEQUENCE; DATA MINING; DATABASES, FACTUAL; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; SYSTEMS BIOLOGY;

EID: 80054078476     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.75     Document Type: Article

References (25)

1. Aniba MR, Poch O, Thompson JD (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res 38: 7353-7363
2. Arthur D, Vassilvitskii S (2007) k-means++: the advantages of careful seeding. Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms. pp 1027-1035
3. Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG (2010) Sequence emBedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 5: 21
4. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast statistical alignment. PLoS Comput Biol 5: e1000392
5. Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java alignment editor. Bioinformatics 20: 426-427 (Pubitemid 38262778)
6. Do CB, MahabhashyamMSP, BrudnoM, BatzoglouS (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15: 330-340 (Pubitemid 40309398)
7. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763 (Pubitemid 28552108)
8. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797 (Pubitemid 38832724)
9. Edgar RC (2010) Quality measures for protein alignment benchmarks. Nucleic Acids Res 38: 2145-2153
10. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2009) The Pfam protein families database. Nucleic Acids Res 38: D211-D222
11. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224
12. Hogeweg P, Hesper B (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20: 175-186 (Pubitemid 14058167)
13. 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 (Pubitemid 34851225)
14. Katoh K, Toh H (2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23, 372-374. (Pubitemid 46323161)
15. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948 (Pubitemid 350162903)
16. Lassmann T, Sonnhammer ELL (2005) Kalign-an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298
17. Liu Y, Schmidt B, Maskell DL (2010) MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior robabilities. Bioinformatics 26: 1958-1964
18. Löytynoja A, Goldman N (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635 (Pubitemid 351931252)
19. Mizuguchi K, Deane CM, Blundell TL, Overington JP (1998) HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 7: 2469-2471 (Pubitemid 28506965)
20. Morgenstern B, Frech K, Dress A, Werner T (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14: 290-294 (Pubitemid 28395866)
21. Notredame C, Higgins DG, Heringa J (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217
22. PirovanoW, Feenstra KA, Heringa J (2008) PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 24: 492-497 (Pubitemid 351256292)
23. Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960 (Pubitemid 40467915)
24. Thompson JD, Koehl P, Ripp R, Poch O (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 61: 127-136 (Pubitemid 41263414)
25. Wilm A, Higgins DG, Notredame C (2008) R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res 36: e52