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A model of evolution and structure for multiple sequence alignment
We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
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The Royal Society
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592536/ https://www.ncbi.nlm.nih.gov/pubmed/18852103 http://dx.doi.org/10.1098/rstb.2008.0170 |
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author | Löytynoja, Ari Goldman, Nick |
author_facet | Löytynoja, Ari Goldman, Nick |
author_sort | Löytynoja, Ari |
collection | PubMed |
description | We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. Furthermore, the evolutionary modelling of substitution process permits adjusting the sensitivity and specificity of the alignment and, if high specificity is aimed at, leaving sequences unaligned when their divergence is beyond a meaningful detection of homology. |
format | Text |
id | pubmed-2592536 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-25925362008-12-29 A model of evolution and structure for multiple sequence alignment Löytynoja, Ari Goldman, Nick Philos Trans R Soc Lond B Biol Sci Research Article We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. Furthermore, the evolutionary modelling of substitution process permits adjusting the sensitivity and specificity of the alignment and, if high specificity is aimed at, leaving sequences unaligned when their divergence is beyond a meaningful detection of homology. The Royal Society 2008-10-07 2008-12-27 /pmc/articles/PMC2592536/ /pubmed/18852103 http://dx.doi.org/10.1098/rstb.2008.0170 Text en Copyright © 2008 The Royal Society http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Löytynoja, Ari Goldman, Nick A model of evolution and structure for multiple sequence alignment |
title | A model of evolution and structure for multiple sequence alignment |
title_full | A model of evolution and structure for multiple sequence alignment |
title_fullStr | A model of evolution and structure for multiple sequence alignment |
title_full_unstemmed | A model of evolution and structure for multiple sequence alignment |
title_short | A model of evolution and structure for multiple sequence alignment |
title_sort | model of evolution and structure for multiple sequence alignment |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592536/ https://www.ncbi.nlm.nih.gov/pubmed/18852103 http://dx.doi.org/10.1098/rstb.2008.0170 |
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