Page ViralGenomes

Non-collinear alignments of viral genomes

Introduction

This is part of advanced algorithms in bioinformatics: genome comparison. I would like to study genome rearrangements, horizontal gene transfer etc. in viruses using non-collinear alignments programs. This might be useful to infer phylogenies, and to depict relations.

The evolutionary history of Bacteriophages seems especially hard to reconstruct, maybe whole genome alignments can help gain some insights.

Software: In order to define a distance measure, the results of the SuperMap /S-LAGAN are probably useful. I will use CHAOS as included with S-LAGAN. or maybe the local Swift implemenentation from Birte, but need to check, whether I can integrate it with S-LAGAN. (Earlier I planned to use ABA for global alignment and BlastZ for local matches.)

References

Just a start:

Complete Genome Viral Phylogenies Suggests the Concerted Evolution of Regulatory Cores and Accessory Satellites.

Transformation distances: a family of dissimilarity measures based on movements of segments

Evolutionary history of bacteriophages with double-stranded DNA genomes

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