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Automatic extraction of reliable regions from multiple sequence alignments
BACKGROUND: High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets while the accuracy of individual alignments is often overlooked. RESULTS: We ha...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892097/ https://www.ncbi.nlm.nih.gov/pubmed/17570868 http://dx.doi.org/10.1186/1471-2105-8-S5-S9 |
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author | Lassmann, Timo Sonnhammer, Erik LL |
author_facet | Lassmann, Timo Sonnhammer, Erik LL |
author_sort | Lassmann, Timo |
collection | PubMed |
description | BACKGROUND: High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets while the accuracy of individual alignments is often overlooked. RESULTS: We have previously developed a method to automatically assess the accuracy and overall difficulty of multiple alignments. This was achieved by a per-residue comparison between alternate alignments of the same sequences. Here we present a key extension to this method, an algorithm to extract similarly aligned regions from several alignments and merge them into a new consensus alignment. CONCLUSION: We demonstrate that the fraction of correctly aligned residues within the resulting alignments is increased by 25 – 100 percent compared to the original input alignments, as only the most reliably aligned parts are considered. |
format | Text |
id | pubmed-1892097 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18920972007-06-15 Automatic extraction of reliable regions from multiple sequence alignments Lassmann, Timo Sonnhammer, Erik LL BMC Bioinformatics Research BACKGROUND: High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets while the accuracy of individual alignments is often overlooked. RESULTS: We have previously developed a method to automatically assess the accuracy and overall difficulty of multiple alignments. This was achieved by a per-residue comparison between alternate alignments of the same sequences. Here we present a key extension to this method, an algorithm to extract similarly aligned regions from several alignments and merge them into a new consensus alignment. CONCLUSION: We demonstrate that the fraction of correctly aligned residues within the resulting alignments is increased by 25 – 100 percent compared to the original input alignments, as only the most reliably aligned parts are considered. BioMed Central 2007-05-24 /pmc/articles/PMC1892097/ /pubmed/17570868 http://dx.doi.org/10.1186/1471-2105-8-S5-S9 Text en Copyright © 2007 Lassmann and Sonnhammer; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Lassmann, Timo Sonnhammer, Erik LL Automatic extraction of reliable regions from multiple sequence alignments |
title | Automatic extraction of reliable regions from multiple sequence alignments |
title_full | Automatic extraction of reliable regions from multiple sequence alignments |
title_fullStr | Automatic extraction of reliable regions from multiple sequence alignments |
title_full_unstemmed | Automatic extraction of reliable regions from multiple sequence alignments |
title_short | Automatic extraction of reliable regions from multiple sequence alignments |
title_sort | automatic extraction of reliable regions from multiple sequence alignments |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892097/ https://www.ncbi.nlm.nih.gov/pubmed/17570868 http://dx.doi.org/10.1186/1471-2105-8-S5-S9 |
work_keys_str_mv | AT lassmanntimo automaticextractionofreliableregionsfrommultiplesequencealignments AT sonnhammererikll automaticextractionofreliableregionsfrommultiplesequencealignments |