ERVsearch

Full documentation is available via ReadTheDocs.

ERVsearch is a pipeline for identification of endogenous retrovirus like regions in a host genome, based on sequence similarity to known retroviruses.

ERVsearch screens for endogenous retrovirus (ERV) like regions in any FASTA file using the Exonerate algorithm (Slater and Birney, 2005, doi:10.1186/1471-2105-6-31).

• In the Screen section, open reading frames (ORFs) resembling retroviral gag, pol and env genes are identified based on their level of similarity to a database of known complete or partial retroviral ORFs.
• In the Classify section, these ORFs are classified into groups based on a database of currently classified retroviruses and phylogenetic trees are built.
• In the ERVRegions section, regions with ORFs resembling more than one retroviral gene are identified.

This is a updated and expanded version of the pipeline used to identify ERVs in Brown and Tarlinton 2017 (doi: 10.1111/mam.12079), Brown et al. 2014 (doi: 10.1128/JVI.00966-14), Brown et al. 2012 (doi: j.virol.2012.07.010) and Tarlinton et al. 2012 (doi: 10.1016/j.tvjl.2012.08.011). The original version is available here as a Perl pipeline and was written by Dr Richard Emes.