Chauve2008

CREATED: 200812290230 LINK: url:~/Modules/Literature/Chauve2008.pdf Framework for reconstruction of contiguous regions of ancestral genomes and application to mammalian genomes

compute a set of possible ancestral syntenic groups, weighted according to conservation in extant species

• gene teams with no gaps
• non-ambiguous unsigned adjacencies
• approximate common intervals
• result is a set S of m weighted and pairwise different ancestral syntenies
• S is encoded as a m x n 0/1 matrix M where M[i,j] = 1 if if marker j belongs to S_i

group and order genomic markers into sets of CARs (Contiguous Ancestral Region)

• consecutive ones property of M
• all C1P ordering of M can be represented as a PQ-tree
• clearing ambiguities by removing syntenies with low weight

comparison with method of Ma et al.