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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Bibliographic Details
Published in:Protein science Vol. 27; no. 1; pp. 135 - 145
Main Authors: Sievers, Fabian, Higgins, Desmond G.
Format: Journal Article
Language:English
Published: United States Wiley Subscription Services, Inc 01.01.2018
John Wiley and Sons Inc
Subjects:
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
Online Access:Get full text
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Description
Summary: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.
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ISSN:0961-8368
1469-896X
1469-896X
DOI:10.1002/pro.3290