Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- PMID: 21988835
- PMCID: PMC3261699
- DOI: 10.1038/msb.2011.75
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Abstract
Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.
Conflict of interest statement
The authors declare that they have no conflict of interest.
Figures
![Figure 1](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/3261699/bin/msb201175-f1.gif)
![Figure 2](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/3261699/bin/msb201175-f2.gif)
![Figure 3](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/3261699/bin/msb201175-f3.gif)
Similar articles
-
Towards the accurate alignment of over a million protein sequences: Current state of the art.Curr Opin Struct Biol. 2023 Jun;80:102577. doi: 10.1016/j.sbi.2023.102577. Epub 2023 Apr 1. Curr Opin Struct Biol. 2023. PMID: 37012200 Review.
-
The Clustal Omega Multiple Alignment Package.Methods Mol Biol. 2021;2231:3-16. doi: 10.1007/978-1-0716-1036-7_1. Methods Mol Biol. 2021. PMID: 33289883
-
Clustal Omega for making accurate alignments of many protein sequences.Protein Sci. 2018 Jan;27(1):135-145. doi: 10.1002/pro.3290. Epub 2017 Oct 30. Protein Sci. 2018. PMID: 28884485 Free PMC article.
-
Multiple sequence alignments.Curr Opin Struct Biol. 2005 Jun;15(3):261-6. doi: 10.1016/j.sbi.2005.04.002. Curr Opin Struct Biol. 2005. PMID: 15963889 Review.
-
Using CLUSTAL for multiple sequence alignments.Methods Enzymol. 1996;266:383-402. doi: 10.1016/s0076-6879(96)66024-8. Methods Enzymol. 1996. PMID: 8743695
Cited by
-
Two genes encoding caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) are candidate genes for physical seed dormancy in cowpea (Vigna unguiculata (L.) Walp.).Theor Appl Genet. 2024 Jun 4;137(7):146. doi: 10.1007/s00122-024-04653-6. Theor Appl Genet. 2024. PMID: 38834825
-
Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae).Sci Rep. 2024 Jun 4;14(1):12861. doi: 10.1038/s41598-024-63584-w. Sci Rep. 2024. PMID: 38834792 Free PMC article.
-
Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB.mLife. 2022 Jun 15;1(2):114-130. doi: 10.1002/mlf2.12030. eCollection 2022 Jun. mLife. 2022. PMID: 38817677 Free PMC article.
-
Investigating the physiological role of S199A and S199D mutants of PHF6 protein in T-cell acute lymphoblastic leukemia.Turk J Med Sci. 2023 Aug 11;53(5):1234-1243. doi: 10.55730/1300-0144.5689. eCollection 2023. Turk J Med Sci. 2023. PMID: 38812997 Free PMC article.
-
Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis.Front Microbiol. 2024 May 15;15:1335310. doi: 10.3389/fmicb.2024.1335310. eCollection 2024. Front Microbiol. 2024. PMID: 38812687 Free PMC article.
References
-
- 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
-
- Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java alignment editor. Bioinformatics 20: 426–427 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources