A cross-species alignment tool (CAT)

• Author(s) / Creator(s)

  • Guan, L.
  • Guo, Y.
  • Liu, T.
  • Li, H.
  • Wang, J.
  • Zheng, W.M.
  • Wong, G.K.

• 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/ webcite. 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.

• Date created

  2007

• Subjects / Keywords

  • Sequences
  • Databases
  • Blast
  • Annotation
  • Programs
  • Genomic DNA
  • Search

• Type of Item

  Article (Published)

• DOI

  https://doi.org/10.7939/R3599Z555

• License

  © 2007 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.