TIRfinder: a web tool for mining class ii transposons carrying terminal inverted repeats

Tomasz Gambin , Michał Startek , Krzysztof Walczak , Jarosław Paszek , Dariusz Grzebelus , Anna Gambin

Abstract

Transposable elements (TEs) can be found in virtually all known genomes; plant genomes are exceptionally rich in this kind of dispersed repetitive sequences. Current knowledge on TE proliferation dynamics places them among the main forces of molecular evolution. Therefore efficient tools to analyze TE distribution in genomes are needed that would allow for comparative genomics studies and for studying TE dynamics in a genome. This was our main motivation underpinning TIRfinder construction—an efficient tool for mining class II TEs carrying terminal inverted repeats. TIRfinder takes as an input a genomic sequence and information on structural properties of a TE family, and identifies all TEs in the genome showing the desired structural characteristics. The efficiency and small memory requirements of our approach stem from the use of suffix trees to identify all DNA segments surrounded by user-specified terminal inverse repeats (TIR) and target site duplications (TSD) which together constitute a mask. On the other hand, the flexibility of the notion of the TIR/TSD mask makes it possible to use the tool for de novo detection. The main advantages of TIRfinder are its speed, accuracy and convenience of use for biologists. A web-based interface is freely available at http://bioputer.mimuw.edu.pl/tirfindertool/.
Author Tomasz Gambin
Tomasz Gambin,,
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, Michał Startek
Michał Startek,,
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, Krzysztof Walczak
Krzysztof Walczak,,
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, Jarosław Paszek
Jarosław Paszek,,
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, Dariusz Grzebelus (FoH / DoGPBaSS)
Dariusz Grzebelus,,
- Department of Genetics, Plant Breeding and Seed Science
, Anna Gambin
Anna Gambin,,
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Journal seriesEvolutionary Bioinformatics, ISSN 1176-9343, (A 25 pkt)
Issue year2013
Vol9
Pages17-27
Publication size in sheets0.5
Keywords in Englishtransposon, terminal inverted repeat, suffix tree, comparative genomics
ASJC Classification1706 Computer Science Applications; 1311 Genetics; 1105 Ecology, Evolution, Behavior and Systematics
DOIDOI:10.4137/EBO.S10619
URL http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562082/
Internal identifierWBIO/2013/112
Languageen angielski
Score (nominal)25
Score sourcejournalList
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2013 = 0.397; WoS Impact Factor: 2013 = 1.169 (2) - 2013=1.706 (5)
Citation count*
Additional fields
FiansowanieThis work was partially supported by Polish Ministry of Science and Educations grant N301 013436, and European Social Fund (UDA-POKL.04.01.01-00-072/09-00 and UDA-POKL.04.01.01-00-051/10-00).
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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