TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats

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/.

[1]  Gary Benson,et al.  Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. , 2004, Genome research.

[2]  Casey M. Bergman,et al.  Discovering and detecting transposable elements in genome sequences , 2007, Briefings Bioinform..

[3]  J. Casacuberta,et al.  Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana. , 2002, Molecular biology and evolution.

[4]  Slawomir Lasota,et al.  Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula , 2007, BMC Genomics.

[5]  Céline Loot,et al.  Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes , 2008, Genetics.

[6]  Jacques Nicolas,et al.  Genome analysis Suffix-tree analyser ( STAN ) : looking for nucleotidic and peptidic patterns in chromosomes , 2005 .

[7]  Stefan Kurtz,et al.  LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons , 2008, BMC Bioinformatics.

[8]  Jason S. Caronna,et al.  Computational prediction and molecular confirmation of Helitron transposons in the maize genome , 2008, BMC Genomics.

[9]  Guojun Yang,et al.  MAK, a computational tool kit for automated MITE analysis , 2003, Nucleic Acids Res..

[10]  Anna Gambin,et al.  Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. , 2009, Gene.

[11]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[12]  F. Zhou,et al.  MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. , 2009, Gene.

[13]  M. Batzer,et al.  Repetitive Elements May Comprise Over Two-Thirds of the Human Genome , 2011, PLoS genetics.

[14]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[15]  J. Jurka,et al.  A universal classification of eukaryotic transposable elements implemented in Repbase , 2008, Nature Reviews Genetics.

[16]  Stefan Kurtz,et al.  REPuter: fast computation of maximal repeats in complete genomes , 1999, Bioinform..

[17]  J. Bennetzen,et al.  A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.

[18]  R. Britten.  Transposable element insertions have strongly affected human evolution , 2010, Proceedings of the National Academy of Sciences.

[19]  S Wright,et al.  Transposon diversity in Arabidopsis thaliana. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Susan R. Wessler,et al.  MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences , 2010, Nucleic acids research.

[21]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[22]  A. Cornish-Bowden.  Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. , 1985, Nucleic acids research.

[23]  S. Eddy,et al.  Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.