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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.

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