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Open Access Methodology article

A cross-species alignment tool (CAT)

Heng Li1234, Liang Guan1245, Tao Liu12, Yiran Guo14, Wei-Mou Zheng123*, Gane Ka-Shu Wong126* and Jun Wang1278*

Author Affiliations

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

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BMC Bioinformatics 2007, 8:349  doi:10.1186/1471-2105-8-349

Published: 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 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.