In:
BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2007-12)
Abstract:
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 .
Type of Medium:
Online Resource
ISSN:
1471-2105
DOI:
10.1186/1471-2105-8-349
Language:
English
Publisher:
Springer Science and Business Media LLC
Publication Date:
2007
detail.hit.zdb_id:
2041484-5
SSG:
12
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