<p>Hello, I have a question for you guys. The perl script rfam_scan.pl uses the program cmsearch to look for a CM model. Wouldn&#39;t be better to use cmscan instead of cmsearch? According to the Infernal manual, we should use cmscan if we have a set of sequences and we wanna know the corresponding or closest CM. Don&#39;t you think so?</p>

As far as I recall, cmscan (like hmmscan) and cmsearch (like hmmsearch) return the exact same results. The big difference is that the former can't be parallelized without special effort.

Edit. http://selab.janelia.org/people/eddys/blog/?p=424