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A cross-species alignment tool (CAT)

BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sen...

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Autores principales: Li, Heng, Guan, Liang, Liu, Tao, Guo, Yiran, Zheng, Wei-Mou, Wong, Gane Ka-Shu, Wang, Jun
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082505/
https://www.ncbi.nlm.nih.gov/pubmed/17880681
http://dx.doi.org/10.1186/1471-2105-8-349
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author Li, Heng
Guan, Liang
Liu, Tao
Guo, Yiran
Zheng, Wei-Mou
Wong, Gane Ka-Shu
Wang, Jun
author_facet Li, Heng
Guan, Liang
Liu, Tao
Guo, Yiran
Zheng, Wei-Mou
Wong, Gane Ka-Shu
Wang, Jun
author_sort Li, Heng
collection PubMed
description BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at . CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and sim4, with the sensitivity of the best inter-species tools, like GeneWise.
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spelling pubmed-20825052007-11-21 A cross-species alignment tool (CAT) Li, Heng Guan, Liang Liu, Tao Guo, Yiran Zheng, Wei-Mou Wong, Gane Ka-Shu Wang, Jun BMC Bioinformatics Methodology Article BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at . CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and sim4, with the sensitivity of the best inter-species tools, like GeneWise. BioMed Central 2007-09-19 /pmc/articles/PMC2082505/ /pubmed/17880681 http://dx.doi.org/10.1186/1471-2105-8-349 Text en Copyright © 2007 Li et al; 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 Methodology Article
Li, Heng
Guan, Liang
Liu, Tao
Guo, Yiran
Zheng, Wei-Mou
Wong, Gane Ka-Shu
Wang, Jun
A cross-species alignment tool (CAT)
title A cross-species alignment tool (CAT)
title_full A cross-species alignment tool (CAT)
title_fullStr A cross-species alignment tool (CAT)
title_full_unstemmed A cross-species alignment tool (CAT)
title_short A cross-species alignment tool (CAT)
title_sort cross-species alignment tool (cat)
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082505/
https://www.ncbi.nlm.nih.gov/pubmed/17880681
http://dx.doi.org/10.1186/1471-2105-8-349
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