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Nucleic Acids Research 2006 34(Web Server issue):W708-W713; doi:10.1093/nar/gkl263
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats

Gábor Tóth*, Gábor Deák, Endre Barta and György B. Kiss

Agricultural Biotechnology Center, Gödöllo Szent-Györgyi Albert u. 4, H-2100, Hungary

*To whom correspondence should be addressed. Tel: +36 28 526224; Fax: +36 28 526101; Email: tothg{at}abc.hu

Received February 14, 2006. Revised March 1, 2006. Accepted March 31, 2006.

Identification of dispersed or interspersed repeats, most of which are derived from transposons, retrotransposons or retrovirus-like elements, is an important step in genome annotation. Software tools that compare genomic sequences with precompiled repeat reference libraries using sensitive similarity-based methods provide reliable means of finding the positions of fragments homologous to known repeats. However, their output is often incomplete and fragmented owing to the mutations (nucleotide substitutions, deletions or insertions) that can result in considerable divergence from the reference sequence. Merging these fragments to identify the whole region that represents an ancient copy of a mobile element is challenging, particularly if the element is large and suffered multiple deletions or insertions. Here we report PLOTREP, a tool designed to post-process results obtained by sequence similarity search and merge fragments belonging to the same copy of a repeat. The software allows rapid visual inspection of the results using a dot-plot like graphical output. The web implementation of PLOTREP is available at http://bioinformatics.abc.hu/PLOTREP/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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[Abstract] [Full Text] [PDF]


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