Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
Reversal and transposition medians
Theoretical Computer Science
A whole genome simulator of prokaryote genome evolution
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
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We present a systematical methodology to refine orthologs identification generated by 3rd party de novo prediction programs and reconstruction of ancestral bacteria genome with this information by a neighboring gene pairs (NGPs) based method. The refinement method combined phylogeny and local gene synteny to improve homology prediction and the reconstruction is focused on both gene content and conserved blocks. Despite the common believe that gene order are much less conserved in prokaryotes, we have applied this method to Rhizobiales, an order of alpha proteobacteria, and show that a reasonable number of large conserved syntenic blocks can still be reconstructed.