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
AbstractTransposable 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/.
|Journal series||Evolutionary Bioinformatics, ISSN 1176-9343, (A 25 pkt)|
|Publication size in sheets||0.5|
|Keywords in English||transposon, terminal inverted repeat, suffix tree, comparative genomics|
|ASJC Classification||; ;|
|Publication indicators||: 2013 = 0.397; : 2013 = 1.169 (2) - 2013=1.706 (5)|
|Fiansowanie||This 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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