Fast and robust multiple sequence alignment with phylogeny-aware gap placement

Fast and robust multiple sequence alignment with phylogeny-aware gap placement

<p>Abstract</p> <p>Background</p> <p>ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide...

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Main Author: Szalkowski Adam M
Format: Article
Language:English
Published: BMC 2012-06-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/13/129
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spelling doaj-b879fa0a99694d9b8932e9c0307653562020-11-24T22:09:12ZengBMCBMC Bioinformatics1471-21052012-06-0113112910.1186/1471-2105-13-129Fast and robust multiple sequence alignment with phylogeny-aware gap placementSzalkowski Adam M<p>Abstract</p> <p>Background</p> <p>ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree.</p> <p>Results</p> <p>This is achieved by incorporating a graph-based sequence representation combined with the advantages of the phylogeny-aware gap placement algorithm of Prank. Further, we account for variations in the substitution pattern by implementing context-specific profiles as in CS-Blast and by estimating amino acid frequencies from input data.</p> <p>Conclusions</p> <p>ProGraphMSA shows good performance and competitive execution times in various benchmarks.</p> http://www.biomedcentral.com/1471-2105/13/129
collection DOAJ
language English
format Article
sources DOAJ
author Szalkowski Adam M
spellingShingle Szalkowski Adam M
Fast and robust multiple sequence alignment with phylogeny-aware gap placement
BMC Bioinformatics
author_facet Szalkowski Adam M
author_sort Szalkowski Adam M
title Fast and robust multiple sequence alignment with phylogeny-aware gap placement
title_short Fast and robust multiple sequence alignment with phylogeny-aware gap placement
title_full Fast and robust multiple sequence alignment with phylogeny-aware gap placement
title_fullStr Fast and robust multiple sequence alignment with phylogeny-aware gap placement
title_full_unstemmed Fast and robust multiple sequence alignment with phylogeny-aware gap placement
title_sort fast and robust multiple sequence alignment with phylogeny-aware gap placement
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2012-06-01
description <p>Abstract</p> <p>Background</p> <p>ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree.</p> <p>Results</p> <p>This is achieved by incorporating a graph-based sequence representation combined with the advantages of the phylogeny-aware gap placement algorithm of Prank. Further, we account for variations in the substitution pattern by implementing context-specific profiles as in CS-Blast and by estimating amino acid frequencies from input data.</p> <p>Conclusions</p> <p>ProGraphMSA shows good performance and competitive execution times in various benchmarks.</p>
url http://www.biomedcentral.com/1471-2105/13/129
work_keys_str_mv AT szalkowskiadamm fastandrobustmultiplesequencealignmentwithphylogenyawaregapplacement
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