Question: Rfam, cmsearch and cmscan
1
gravatar for int11ap1
4.3 years ago by
int11ap1310
Barcelona
int11ap1310 wrote:

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?

cmscan cmsearch rfam • 4.1k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 4.3 years ago by int11ap1310
5
gravatar for Rfammer
4.2 years ago by
Rfammer50
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 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.

ADD COMMENTlink written 4.2 years ago by Rfammer50
2
gravatar for 5heikki
4.2 years ago by
5heikki7.4k
Finland
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. 

 

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

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