Clustal Omega for making accurate alignments of many protein sequences

Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently desc...

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Vydané v:	Protein science Ročník 27; číslo 1; s. 135 - 145
Hlavní autori:	Sievers, Fabian, Higgins, Desmond G.
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States Wiley Subscription Services, Inc 01.01.2018 John Wiley and Sons Inc
Predmet:	Alignment benchmarking Benchmarks clustal omega multiple sequence alignment Nucleotide sequence Protein structure Proteins Proteins - chemistry Proteins - genetics Secondary structure Sequence Alignment - methods Sequence Analysis, Protein - methods Software Tools for Protein Science protein structure clustal omega benchmarking multiple sequence alignment
ISSN:	0961-8368, 1469-896X, 1469-896X
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Abstract	Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on‐line from a variety of sites, especially the EBI www.ebi.ac.uk.
AbstractList	Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on-line from a variety of sites, especially the EBI www.ebi.ac.uk.Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on-line from a variety of sites, especially the EBI www.ebi.ac.uk. Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on-line from a variety of sites, especially the EBI www.ebi.ac.uk. Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on‐line from a variety of sites, especially the EBI www.ebi.ac.uk .
Author	Sievers, Fabian Higgins, Desmond G.
AuthorAffiliation	1 School of Medicine and Conway Institute of Biomolecular and Biomedical Research University College Dublin Belfield Dublin 4 Ireland
AuthorAffiliation_xml	– name: 1 School of Medicine and Conway Institute of Biomolecular and Biomedical Research University College Dublin Belfield Dublin 4 Ireland
Author_xml	– sequence: 1 givenname: Fabian surname: Sievers fullname: Sievers, Fabian organization: University College Dublin – sequence: 2 givenname: Desmond G. orcidid: 0000-0002-3952-3285 surname: Higgins fullname: Higgins, Desmond G. email: Des.higgins@ucd.ie organization: University College Dublin
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/28884485$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1093/nar/gkv332 10.1093/bioinformatics/bti125 10.1038/msb.2011.75 10.1093/nar/gki541 10.1093/nar/gkr367 10.1093/nar/gkt1223 10.1371/journal.pone.0009490 10.1093/nar/gkf436 10.1093/nar/gki198 10.1002/prot.20527 10.1093/nar/25.24.4876 10.1093/bioinformatics/btw840 10.1093/nar/22.22.4673 10.1186/1748-7188-5-21 10.1093/nar/27.13.2682 10.1186/1471-2105-15-338 10.1002/pro.5560071126 10.1006/jmbi.2000.4042 10.1073/pnas.1405628111 10.1093/bioinformatics/btv592 10.1111/j.1574-6941.2006.00060.x 10.1038/newbio245232a0
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Snippet	Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some...
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SubjectTerms	Alignment benchmarking Benchmarks clustal omega multiple sequence alignment Nucleotide sequence Protein structure Proteins Proteins - chemistry Proteins - genetics Secondary structure Sequence Alignment - methods Sequence Analysis, Protein - methods Software Tools for Protein Science
Title	Clustal Omega for making accurate alignments of many protein sequences
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