is updating is moving off of Janelia tonight, into the great cloud. You may see some flakiness as DNS nameservers update.

7 thoughts on “ is updating

  1. Hello,

    I would like to query assembled nucleotide reads (short contigs) against the Pfam HMM database in order to detect Pfam protein domains on the contigs. I tried using nhmmscan for the same. There are some errors while parsing the database which do not occur with hmmscan. I get the “segmentation fault” error after running it.


    • nhmmscan is for DNA/DNA comparison.

      We currently don’t have a program that does translated search in either direction (either protein HMM query vs DNA database, or DNA HMM query against a protein profile database). Instead you need to translate your DNA reads yourself in all six frames, and search that database with Pfam.

      Shouldn’t seg fault, of course; I think we’ve already fixed this problem in the dev code, will check.


  2. Thanks a lot for the quick reply! Okay, I will query the translated DNA sequences. Although in the documentation it is written that – nhmmscan can be used for searching nucleotide sequence(s) against a nucleotide profile. Is there a nucleotide profile database available somewhere?


  3. Yes. Dfam ( for example.

    Not sure what you meant about the documentation when you said “although”. The documentation is correct, nhmmscan is for DNA/DNA comparison, and that’s also what I said above. If you’re searching DNA sequences against Pfam, Pfam is a protein profile database.


  4. Hello,

    I am trying to download the HMMER today but getting no response from the server when I clicked “download”. Same thing in the “Alternative Download Options”. Can you please fix that?

    Thank you!


    • The standard advice to all questions like this: network glitches (at your end, or ours) are fairly common, so first thing to do is wait a while and try again. Downloads are working fine at our end; I just checked.


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