Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

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

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      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/.

      Related collections

      Most cited references 24

      • Record: found
      • Abstract: found
      • Article: not found

      Basic local alignment search tool.

      A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
        Bookmark
        • Record: found
        • Abstract: found
        • Article: not found

        Repbase Update, a database of eukaryotic repetitive elements.

        Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          The B73 maize genome: complexity, diversity, and dynamics.

          We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
            Bookmark

            Author and article information

            Affiliations
            [1 ]Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.
            [2 ]College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.
            [3 ]Institute of Informatics, University of Warsaw, Warsaw, Poland.
            [4 ]Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Krakow, Poland.
            [5 ]Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland.
            Author notes
            Corresponding author email: tgambin@ 123456ii.pw.edu.pl
            Journal
            Evol Bioinform Online
            Evol. Bioinform. Online
            101256319
            Evolutionary Bioinformatics Online
            Libertas Academica
            1176-9343
            2013
            22 January 2013
            : 9
            : 17-27
            3562082
            10.4137/EBO.S10619
            ebo-9-2013-017
            © 2013 the author(s), publisher and licensee Libertas Academica Ltd.

            This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.

            Categories
            Software Review

            Comments

            Comment on this article