Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except when it makes sense biologically, we recommend ignoring the hits covering less than half of the profile.
This software is now part of two modules for MacSyFinder. The T4SS for protein secretion can be identified using TXSScan. The CONJscan part is now a module in MacSyFinder.
Authors: Eduardo Rocha, Julien Guglielmini (for the original version), Jean Cury (for the MacSyFinder version). Bertrand Néron and Olivia have made the Galaxy version. Sophie Abby for MacSyFinder and TXSScan.
Availability on Galaxy (CONJscan):https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fodoppelt%2Fconjscan%2FConjScan%2F1.0.2
Availability on Galaxy (TXSScan):https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fodoppelt%2Fconjscan%2FConjScan%2F1.0.2
MacSyFinder (standalone): https://github.com/gem-pasteur/macsyfinder