Gene teams: a new formalization of gene clusters for comparative genomics.
This paper describes an efficient algorithm based on a new concept called gene team for detecting conserved gene clusters among an arbitrary number of chromosomes. Within the clusters, neither the order of the genes nor their orientation need be conserved. In addition, insertion of foreign genes within the clusters are permitted to a user-defined extent. This algorithm has been implemented in a publicly available TEAM software that proves to be an efficient tool for systematic searches of conserved gene clusters. Examples of actual biological results are provided. The software is downloadable from http://www-igm.univ-mlv.fr/ approximately raffinot/geneteam.html.
Luc
Nicolas
N
CNRS - Laboratoire Génome et Informatique, Tour Evry 2, 523, Place des Terrasses de 1'Agora, 91034 Evry, France.
Risler
Jean-Loup
JL
Bergeron
Anne
A
Raffinot
Mathieu
M
D000465:Algorithms; D017124:Conserved Sequence / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics*; D012984:Software