Question: Rfam, cmsearch and cmscan
gravatar for int11ap1
4.3 years ago by
int11ap1310 wrote:

Hello, I have a question for you guys. The perl script 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?

cmscan cmsearch rfam • 4.1k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 4.3 years ago by int11ap1310
gravatar for Rfammer
4.2 years ago by
United Kingdom
Rfammer50 wrote:

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 Historically, 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.

ADD COMMENTlink written 4.2 years ago by Rfammer50
gravatar for 5heikki
4.2 years ago by
5heikki7.4k wrote:

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. 



ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by 5heikki7.4k
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