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?
2 answers
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.
Log in to answer this question.
-
Questions about genome annotation of non-coding RNA with infernal
written by Abieskawa •
-
cutadapt command line
written by kamyasingh90 •
-
Using TargetScan on other species
written by biofalconch
-
indicizing genome in tophat2
written by zizigolu
-
Perl module to handle the CCDS file
written by anp375
-
How to know a program I use is parallelizable?
written by mparadis92 •
-
Is there a Perl script to use Biomart ID conversion?
written by anp375
-
Data management/annotation solutions for microarray and NGS experiments
written by Adamc
-
How do I get gene annotation for probes on Illumina's HM450k arrays in FDb.InfiniumMethylation.hg19?
written by biohack92
-
Methods or packages for identifying differential splicing
written by Daniel Standage
