<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>

<p>Hi there, Rfam project leader here (for verification you can check our Twitter feed; we&#39;ve linked to this question)</p>

<p>Yes, in future we&#39;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.</p>
