Introduction

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.

Publications

  1. A cross-species alignment tool (CAT).
    Cite this
    Li H, Guan L, Liu T, Guo Y, Zheng WM, Wong GK, Wang J, Wang J, 2007-01-01 - BMC bioinformatics

Credits

  1. Heng Li
    Developer

  2. Liang Guan
    Developer

  3. Tao Liu
    Developer

  4. Yiran Guo
    Developer

  5. Wei-Mou Zheng
    Developer

  6. Gane Ka-Shu Wong
    Developer

  7. Jun Wang
    Investigator

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Summary
AccessionBT000226
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByJun Wang