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BMC Bioinformatics. 2007 Sep 19;8:349.

A cross-species alignment tool (CAT).

Author information

1
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China. lh3@sanger.ac.uk

Abstract

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 http://xat.sourceforge.net/.

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.

PMID:
17880681
PMCID:
PMC2082505
DOI:
10.1186/1471-2105-8-349
[Indexed for MEDLINE]
Free PMC Article
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