t2prhd: a tool to study the patterns of repeat evolution

Background: The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. Results: We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats det...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Botond Sipos, Kálmán Somogyi, István Andó, Zsolt Pénzes
• Keywords: BMCBI 2008, Gene Families, Homology Diagrams, Pairwise Repeat Homology