Journal
BIOINFORMATICS
Volume 26, Issue 15, Pages 1897-1898Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btq301
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Funding
- Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior [4676/08-4]
- Conselho Nacional de Desenvolvimento Cientifico e Tecnologico [472504/2007-0, 479207/2007-0, 483177/2009-1]
- ANR [BLAN08-1335497]
- ANR-BBSRC [ANR-07-BSYS 003 02]
- ERC Advanced Grant Sisyphe
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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.
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