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

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

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

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/.

Original languageEnglish
Pages (from-to)W708-W713
JournalNucleic acids research
Volume34
Issue numberWEB. SERV. ISS.
DOIs
Publication statusPublished - Jul 1 2006

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ASJC Scopus subject areas

  • Genetics

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