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PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences
In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA s...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125727/ https://www.ncbi.nlm.nih.gov/pubmed/21515632 http://dx.doi.org/10.1093/nar/gkr244 |
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author | Sahraeian, Sayed Mohammad Ebrahim Yoon, Byung-Jun |
author_facet | Sahraeian, Sayed Mohammad Ebrahim Yoon, Byung-Jun |
author_sort | Sahraeian, Sayed Mohammad Ebrahim |
collection | PubMed |
description | In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA sequences. Both PicXAA and PicXAA-R are probabilistic non-progressive alignment algorithms that aim to find the optimal alignment of multiple biological sequences by maximizing the expected accuracy. PicXAA and PicXAA-R greedily build up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures local similarities among sequences. PicXAA-Web integrates these two algorithms in a user-friendly web platform for accurate alignment and analysis of multiple protein, DNA and RNA sequences. PicXAA-Web can be freely accessed at http://gsp.tamu.edu/picxaa/. |
format | Online Article Text |
id | pubmed-3125727 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31257272011-07-05 PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences Sahraeian, Sayed Mohammad Ebrahim Yoon, Byung-Jun Nucleic Acids Res Articles In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA sequences. Both PicXAA and PicXAA-R are probabilistic non-progressive alignment algorithms that aim to find the optimal alignment of multiple biological sequences by maximizing the expected accuracy. PicXAA and PicXAA-R greedily build up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures local similarities among sequences. PicXAA-Web integrates these two algorithms in a user-friendly web platform for accurate alignment and analysis of multiple protein, DNA and RNA sequences. PicXAA-Web can be freely accessed at http://gsp.tamu.edu/picxaa/. Oxford University Press 2011-07-01 2011-04-22 /pmc/articles/PMC3125727/ /pubmed/21515632 http://dx.doi.org/10.1093/nar/gkr244 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Sahraeian, Sayed Mohammad Ebrahim Yoon, Byung-Jun PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
title | PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
title_full | PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
title_fullStr | PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
title_full_unstemmed | PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
title_short | PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
title_sort | picxaa-web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125727/ https://www.ncbi.nlm.nih.gov/pubmed/21515632 http://dx.doi.org/10.1093/nar/gkr244 |
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