T2prhd: a tool to study the patterns of repeat evolution.

BMC Bioinformatics
Botond SiposZsolt Pénzes

Abstract

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. 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 and is also accessible as an online tool at http:...Continue Reading

References

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Citations

Apr 1, 2009·Briefings in Bioinformatics·Peng Zhou, Zhicai Shang
Jan 14, 2012·Protein Engineering, Design & Selection : PEDS·Steven A JacobsKaryn T O'Neil
Aug 16, 2008·Molecular Biology and Evolution·Kálmán SomogyiIstván Andó

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Datasets Mentioned

BETA
AAB47488.1
CAA39628.1
AAB82015.1

Software Mentioned

xcolor
PHYLIP
fancyhdr
BioPerl
Perl script
CLUSTAL W
Batik
t2prhd
Perl
Pise

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