SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments

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dc.contributor.authorAjawatanawong, P.
dc.contributor.authorAtkinson, G.
dc.contributor.authorWatson-Haigh, N.
dc.contributor.authorMacKenzie, B.
dc.contributor.authorBaldauf, S.
dc.date.issued2012
dc.descriptionFirst published online: June 11, 2012. This article appears in: Web Server issue
dc.description.abstractAnalyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.
dc.description.statementofresponsibilityPravech Ajawatanawong, Gemma C. Atkinson, Nathan S. Watson-Haigh, Bryony MacKenzie and Sandra L. Baldauf
dc.identifier.citationNucleic Acids Research, 2012; 40(W1):W340-W347
dc.identifier.doi10.1093/nar/gks561
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.orcidWatson-Haigh, N. [0000-0002-7935-6151]
dc.identifier.urihttp://hdl.handle.net/2440/86550
dc.language.isoen
dc.publisherOxford University Press
dc.relation.isreplacedby2440/93069
dc.relation.isreplacedbyhttp://hdl.handle.net/2440/93069
dc.rights© The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttps://doi.org/10.1093/nar/gks561
dc.subjectProteins
dc.subjectSequence Alignment
dc.subjectSequence Analysis, Protein
dc.subjectAlgorithms
dc.subjectInternet
dc.subjectSoftware
dc.subjectINDEL Mutation
dc.titleSeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
dc.typeJournal article
pubs.publication-statusPublished

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