Related Experiment Video
Updated: Jun 22, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
Published on: March 22, 2016
RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic
Göran Sperber1, Anders Lövgren, Nils-Einar Eriksson
1Physiology unit, Department of Neuroscience, Box 593, Uppsala, Sweden. goran.sperber@neuro.uu.se
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
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 Concept Videos
Retroviruses
Retrovirus Life Cycles
Size and Structure of Viral Genomes
Non-LTR Retrotransposons
LTR Retrotransposons
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
Viruses with RNA Genomes

