Documentation for the script

Author Martin Madera, with assistance from Julian Gough
Download Nice html or source
Brief desription A converter between SAM3 and HMMER2.0 (multiple-domains per sequence, or local/local) model files
Limitations On the HMMER side, the script only reads (and translates to) multiple-domains per sequence files (intended for a local/local search), i.e. those that would have been created via the (PFAM default) command
$ hmmbuild -f
  1. The SAM hmmconvert program to convert between SAM ascii and binary files
  2. If converting to HMMER2.0, the hmmcalibrate program to calibrate the resultant model (but unlike hmmconvert, hmmcalibrate is not called by this script)
Usage Either
$ model.mod
$ model.hmm
where model.hmm is assumed to be a HMMER2.0 file and model.mod a SAM3 one. The output file is either model.con.hmm or model.con.mod, with model.con.asc.mod also created.
Long description The long description is intended as background information for those intending to understand, modify or extend the script. It is mostly a summary of information about the two file formats which the authors have gathered through reading the SAM and HMMER manuals and sources, interaction with authors of the packages and their own experimentation.