In the latest version of the HMMER website we have focused on enhancing the recognition and display of domains and motifs found in query sequences. To achieve this we added two new features to the site, additional HMM databases and simple motif detection.
We have …
It has been a couple of weeks now since we released jackhmmer on the HMMER website and so far (touch wood etc…), it seems to be performing as we had hoped – here on ‘the farm’ we are getting very excited with the results we are observing.
Have you ever wondered how a new protein family would look in context of other Pfam domains? Well, look no further than the hmmer website! At the end of last week we released a new way of visualizing search results according to ‘domain architecture’ (applies to both phmmer and hmmsearch …
We've had a couple of reports of some less-than-intuitive behavior of HMMER3 on poor-scoring sequences. As one correspondent described it, HMMER3 is stubborn. It will refuse to score and align certain low-scoring sequences no matter what options you try to set. It's probably worth explaining this behavior in public, partly …
From today's email...
Suppose, for example, you want to search 300 million metagenomic sequence reads, each about 200nt long, against the Pfam database. What's the best way to do that task with HMMER3? The bottom line: use hmmsearch, not hmmscan. For the numerology of why (and chapter and verse on …
Over at hmmer.janelia.org, you'll notice a significant change over on the right side of the page. See the "Search" button? You don't have to use HMMER at the UNIX command line any more. Thanks to support from the Howard Hughes Medical Institute, and hard work from Rob Finn …
I've added some sections to the version of the HMMER User's Guide that's linked at hmmer.org. You can download the new Guide from here.
The Guide now briefly describes the HMMER3 acceleration pipeline for profile/sequence comparison, and the methods used to identify domain "envelopes", maximum expected accuracy alignments …
Our quest is at an end.
Monty Python and the Holy Grail
Four years in development, and a year in testing: HMMER3 has reached its first public production release. Do we have time for a beer and a small celebration before we write the manuscripts and move straight on to …
My relationship with email is fraught. On the one hand, it ravages my time and concentration; on the other hand, it's better than the damned phone.
I get too much email to answer, and that makes me feel guilty. Would it help to post a general disclaimer? Often I think …
In a world where "a few days" means a month; in a world where "HMMER3 is ready" means another release candidate: ta-da! A release candidate!
HMMER3 release candidate two is available for download as a source code tarball. Over at hmmer.org, there are also links for downloading tarballs including …