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RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences

1 , 2 , 2 , 3 , , 3

BMC Bioinformatics

BioMed Central

European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration

18–20 September 2008

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      Abstract

      Background

      The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called proviral or endogenous retroviral sequences; ERVs, constitutes at least 5% of vertebrate genomes. After infecting the host, these retroviruses have integrated in germ line cells, and have then been carried in genomes for at least several 100 million years. A better understanding of structure and function of these sequences can have profound biological and medical consequences.

      Methods

      RetroTector © (ReTe) is a platform-independent Java program for identification and characterization of proviral sequences in vertebrate genomes. The full ReTe requires a local installation with a MySQL database. Although not overly complicated, the installation may take some time. A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web.

      Results

      ROL http://www.fysiologi.neuro.uu.se/jbgs/ was implemented under the Batchelor web interface (A Lövgren et al). It allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 10 000 kilobases). Up to ten submissions can be done simultaneously, allowing batch analysis of <= 100 Megabases. Jobs are shown in an IP-number specific list. Results are text files, and can be viewed with the program, RetroTectorViewer.jar (at the same site), which has the full graphical capabilities of the basic ReTe program. A detailed analysis of any retroviral sequences found in the submitted sequence is graphically presented, exportable in standard formats. With the current server, a complete analysis of a 1 Megabase sequence is complete in 10 minutes. It is possible to mask nonretroviral repetitive sequences in the submitted sequence, using host genome specific "brooms", which increase specificity.

      Discussion

      Proviral sequences can be hard to recognize, especially if the integration occurred many million years ago. Precise delineation of LTR, gag, pro, pol and env can be difficult, requiring manual work. ROL is a way of simplifying these tasks.

      Conclusion

      ROL provides 1. annotation and presentation of known retroviral sequences, 2. detection of proviral chains in unknown genomic sequences, with up to 100 Mbase per submission.

      Related collections

      Most cited references 11

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      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.
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        Interspersed repeats and other mementos of transposable elements in mammalian genomes.

         Arian Smit (1999)
        The bulk of the human genome is ultimately derived from transposable elements. Observations in the past year lead to some new and surprising ideas on functions and consequences of these elements and their remnants in our genome. The many new examples of human genes derived from single transposon insertions highlight the large contribution of selfish DNA to genomic evolution.
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          LTR_STRUC: a novel search and identification program for LTR retrotransposons.

          Long terminal repeat (LTR) retrotransposons constitute a substantial fraction of most eukaryotic genomes and are believed to have a significant impact on genome structure and function. Conventional methods used to search for LTR retrotransposons in genome databases are labor intensive. We present an efficient, reliable and automated method to identify and analyze members of this important class of transposable elements. We have developed a new data-mining program, LTR_STRUC (LTR retrotransposon structure program) which identifies and automatically analyzes LTR retrotransposons in genome databases by searching for structural features characteristic of such elements. LTR_STRUC has significant advantages over conventional search methods in the case of LTR retrotransposon families having low sequence homology to known queries or families with atypical structure (e.g. non-autonomous elements lacking canonical retroviral ORFs) and is thus a discovery tool that complements established methods. LTR_STRUC finds LTR retrotransposons using an algorithm that encompasses a number of tasks that would otherwise have to be initiated individually by the user. For each LTR retrotransposon found, LTR_STRUC automatically generates an analysis of a variety of structural features of biological interest. The LTR_STRUC program is currently available as a console application free of charge to academic users from the authors.
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            Author and article information

            Affiliations
            [1 ]Physiology unit, Dpt of Neuroscience, Box 593, Uppsala, Sweden
            [2 ]Linnaeus Centre for Bioinformatics, Biomedical Centre, Box 598, 751 24 Uppsala, Sweden
            [3 ]Section of Virology, Department of Medical Sciences, Uppsala University, Academic Hospital, 751 85 Uppsala, Sweden
            Contributors
            Conference
            BMC Bioinformatics
            BMC Bioinformatics
            BioMed Central
            1471-2105
            2009
            16 June 2009
            : 10
            : Suppl 6
            : S4
            2697651
            19534753
            1471-2105-10-S6-S4
            10.1186/1471-2105-10-S6-S4
            Copyright © 2009 Sperber et al; licensee BioMed Central Ltd.

            This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

            European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration
            Martina Franca, Italy
            18–20 September 2008
            Categories
            Proceedings

            Bioinformatics & Computational biology

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