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Author |
Martin Madera, with assistance from
Julian Gough |
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Download |
Nice html or source |
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Brief desription |
A converter between SAM3 and HMMER2.0 (multiple-domains per sequence, or
local/local)
model files |
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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
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Requirements |
-
The SAM
hmmconvert program to convert between SAM ascii and binary files
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If converting to HMMER2.0, the
hmmcalibrate
program to calibrate the resultant model (but unlike
hmmconvert, hmmcalibrate is not
called by this script)
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Usage |
Either $ convert.pl model.mod
or
$ convert.pl 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.
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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.
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