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Overview

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. SPSconvert 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 SPSpfam.  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 ".sps" identifier.
SPScovert generates an output log with details of the HMM's it processed,  including an HMM length histogram.

SPSpfam

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.
SPSpfam is designed to replace Hmmpfam in scripts such as InterProScan.  To make this substitution transparent SPSpfam looks for the SPS HMM library files without requiring the ".sps" file extension on the command line.  For instance,  converting the HMM library file Pfam_ls to SPS binary creates the library file Pfam_ls.sps.  When the command line
Spspfam  Pfam_ls  is executed SPSpfam first looks for a file named Pfam_ls.sps.  If that search fails it then looks for the file named Pfam_ls.  Therefore, the user can have a text HMM library Pfam_ls and an SPS binary library Pfam_ls.sps both available in the same directory search paths and use SPSpfam and Hmmpfam interchangeably.