7 thoughts on “hmmer.org 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.


    1. 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 (dfam.org) 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!


    1. 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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