Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Ordering partially assembled genomes using gene arrangements
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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There has been a trend in increasing phylogenetic coverage for genome sequencing while decreasing the sequencing coverage for each genome. With lower coverage, there is an increasing number of genomes being published in contig form. Rearrangement algorithms, including gene order-based phylogenetic tools, require whole genome data on gene order, segment order, or some other marker order. Items whose chromosomal location is unknown cannot be part of the input. The question we address here is, for gene order-based phylogenetic analysis, how can we use rearrangement algorithms to handle genomes available in contig form only? Our suggestion is to use the contigs directly in the rearrangement algorithms as if they were chromosomes, while making a number of corrections, e.g., we correct for the number of extra fusion/fission operations required to make contigs comparable to full assemblies. We model the relationship between contig number and genomic distance, and estimate the parameters of this model using insect genome data. With this model, we can then reconstruct the phylogeny based on genomic distance and numbers of contigs.