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 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.
Li
Heng
H
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China. lh3@sanger.ac.uk
Guan
Liang
L
Liu
Tao
T
Guo
Yiran
Y
Zheng
Wei-Mou
WM
Wong
Gane Ka-Shu
GK
Wang
Jun
J
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013045:Species Specificity
D012333:RNA, Messenger