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. Background Gene...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Heng Li, Liang Guan, Tao Liu, Yiran Guo, Wei-Mou Zheng, Gane Ka-Shu Wong, Jun Wang
• Keywords: Algorithms, Alignment Tool, BMCBI 2007, Cross-species Alignment Tool