%0 Journal Article
%T t2prhd: a tool to study the patterns of repeat evolution
%A Botond Sipos
%A K¨˘lm¨˘n Somogyi
%A Istv¨˘n And¨®
%A Zsolt P¨¦nzes
%J BMC Bioinformatics
%D 2008
%I BioMed Central
%R 10.1186/1471-2105-9-27
%X 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 detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd) available for downloading at http://t2prhd.sourceforge.net webcite and is also accessible as an online tool at http://t2prhd.brc.hu webcite. The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III) domain repeats of three selected mammalian Tenascin sequences.Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families), as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of scripts.The conceptual models developed to explain the evolution of multigene families [1,2] have also been applied to sequence repeats inside a gene/protein. Studies of repeat evolution [3-9] have often revealed complex patterns: some repeats may evolve in concert, subject to homogenization, while other repeats may maintain their sequence identity, which is more consistent with birth-and-death and/or divergent evolution. Phylogenetic reconstruction is an established approach with which to study the mode of evolution of multigene families [10-14] and repeats [3-9]. In the analysis of closely related species, the association of genes on the same locus (orthologues) on phylogenetic trees suggests independent evolution of the respective members, as expected for the birth-and-death model. On the contrary, the association o
%U http://www.biomedcentral.com/1471-2105/9/27