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'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't you think so?
Hi there, Rfam project leader here (for verification you can check our Twitter feed; we've linked to this question)
Yes, in future we'll be providing cmscan instead of rfam_scan.pl. Historically, rfam_scan.pl needed to include the BLAST filtering step, which reduced the search space the CM needed to cover, making the problem computationally tractable. However, INFERNAL 1.1 now uses HMM-based filters as part of the cmsearches, meaning the blast filters are redundant.
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.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6