Scaffold filling, contig fusion and comparative gene order inference

Background: There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes? Results: Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert, Steve Rounsley, David Sankoff
• Keywords: Algorithm, BMCBI 2010, Genomes, Scaffold