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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...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2007
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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. |
format | Text |
id | pubmed-2082505 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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