Using SPSpfam 2.3.2
SPSpfam requires a binary HMM library as an input HMM library.
A special pre-processing formatter, SPSconvert, is supplied
to pre-process the textual HMMER2.0 HMM libraries and prepare them for
use by SPSpfam. SPSconvert has no input options; the only
command-line argument required is the name of the HMMER2.0 ASCII library.
automatically creates the SPS binary file by processing the input HMM library
and appending a ".sps" extension to the library name. For example,
to convert the Pfam_ls HMM library to SPS binary you could enter the command:
Spsconvert Pfam_ls SPScovert will produce an
SPS binary called "Pfam_ls.sps", which will later be recognized by
You may also specify an optional second argument to SPScovert as
the target file to which the binary will be written. With this option
the second file is created as specified by the user without appending the
SPSpfam produces output almost always identical to hmmpfam, except
of course for the program identifier and the license information.
The programs have been tested together on a wide range of input data and
so far have produced identical pattern matches. Occasionally the
floating point scores etc. will vary in the decimal places. These
differences are insignificant and have no effect on the final search results.
The SPSpfam input option list includes all of the hmmpfam options
plus one additional feature. SPSpfam includes the capability of
specifying nucleic acid strings as queries to the HMM protein databases.
If the user specifies the -N option
on the command line SPSpfam will assume the input queries are nucleic
acids and generate the six amino acid queries corresponding to the six
possible reading frames produced from the forward and reverse translations
of the nucleic acid queries. SPSpfam also replaces any ambiguous
symbols with N's before producing the translations. In the
output file SPSpfam appends the frame information to the end of
the sequence name as "frame 0 FWD" for the original translated sequence,
"frame 1 FWD" for the one nuceic-acid-shifted translation etc. The
"REV" keyword is used for the reverse complement translated sequences.
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