A cross-species alignment tool (CAT)
- Equal contributors
1 Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
2 James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310008, China
3 Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China
4 Graduate University of the Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100039, China
5 Institute of Computing Technology, Chinese Academy of Science, Beijing 100080, China
6 UW Genome Center, Department of Medicine, University of Washington, Seattle, WA 98195, USA
7 The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark
8 Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark
BMC Bioinformatics 2007, 8:349 doi:10.1186/1471-2105-8-349Published: 19 September 2007
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.
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/ webcite.
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.