nBlog 2009-11-16

HMMER3 is incredibly fast! But ...

Pfam 24.0 has been released at the last month. But the release is not backward compatible with HMMER2 bcause it was built using the the new version of the HMMER package, HMMER3. The new package is still a beta but incredibly fast (over 100-folds)!! So, I started preparations for using the new package. The output format of the new package is quite different. I read the User's Guide to write a parser script for the new package, and found the following phrase:

... don't write any heavy duty output parsers around HMMER3 just yet.
According to Dr. Sean R. Eddy, who made the HMMER package, I will suspend writing new parser until the new package is finalized.