title: A cross-species alignment tool (CAT).
abstract: 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.
authors: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China. lh3@sanger.ac.uk
authors: Heng
authors: H
authors: Li
authors: Liang
authors: L
authors: Guan
authors: Tao
authors: T
authors: Liu
authors: Yiran
authors: Y
authors: Guo
authors: Wei-Mou
authors: WM
authors: Zheng
authors: Gane Ka-Shu
authors: GK
authors: Wong
authors: Jun
authors: J
authors: Wang
mesh_terms: 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
chemical_list: D012333:RNA, Messenger