Introduction

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. RESULT: 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

Publications

  1. RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.
    Cite this
    Sperber G, Lövgren A, Eriksson NE, Benachenhou F, Blomberg J, 2009-01-01 - BMC bioinformatics
  2. Automated recognition of retroviral sequences in genomic data--RetroTector.
    Cite this
    Sperber GO, Airola T, Jern P, Blomberg J, 2007-01-01 - Nucleic acids research

Credits

  1. Göran Sperber
    Developer

  2. Anders Lövgren
    Developer

  3. Nils-Einar Eriksson
    Developer

  4. Farid Benachenhou
    Developer

  5. Jonas Blomberg
    Investigator

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Summary
AccessionBT003727
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJonas Blomberg