Martin Madera, with assistance from
Nice html or source
|| A converter between SAM3 and HMMER2.0 (multiple-domains per sequence, or
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
$ hmmbuild -f
hmmconvert program to convert between SAM ascii and binary files
If converting to HMMER2.0, the
program to calibrate the resultant model (but unlike
hmmcalibrate is not
called by this script)
$ convert.pl model.mod
$ convert.pl model.hmm
model.hmm is assumed to be a HMMER2.0 file and
model.mod a SAM3 one.
The output file is either
model.con.asc.mod also created.
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.