title: Cassis: detection of genomic rearrangement breakpoints.
abstract: CONCLUSIONS
  Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints.
  
  
  BACKGROUND
  Perl and R scripts are freely available for download at http://pbil.univ-lyon1.fr/software/Cassis/. Documentation with methodological background, technical aspects, download and setup instructions, as well as examples of applications are available together with the package. The package was tested on Linux and Mac OS environments and is distributed under the GNU GPL License.
authors.affiliation: Equipe BAMBOO, INRIA Grenoble Rhône-Alpes et Laboratoire de Biométrie et Biologie Evolutive (UMR 5558) CNRS, Université Lyon 1, Villeurbanne, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Baudet
authors.forename: Claire
authors.initials: C
authors.lastname: Lemaitre
authors.forename: Zanoni
authors.initials: Z
authors.lastname: Dias
authors.forename: Christian
authors.initials: C
authors.lastname: Gautier
authors.forename: Eric
authors.initials: E
authors.lastname: Tannier
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Sagot
mesh_terms: D000465:Algorithms; D056905:Chromosome Breakpoints; D002875:Chromosomes / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D016678:Genome / Q000235:genetics*; D011995:Recombination, Genetic; D012984:Software; D026801:Synteny