NAME

       ssematch - Search a DCF file for secondary structure matches.

SYNOPSIS

       ssematch -ssinfile infile -dcfinfile infile [-datafile matrixf] -maxhits integer
                [-rgapopen float] [-rgapextend float] [-egapopen float] [-egapextend float]
                -outssfile outfile -outsefile outfile -logfile outfile

       ssematch -help

DESCRIPTION

       ssematch is a command line program from EMBOSS (“the European Molecular Biology Open
       Software Suite”). It is part of the "Utils:Database creation" command group(s).

OPTIONS

   Input section
       -ssinfile infile
           This option specifies the name of the file of secondary structure (input).

       -dcfinfile infile
           This option specifies the name of the DCF file (domain classification file) (input). A
           'domain classification file' contains classification and other data for domains from
           SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE
           and CATHPARSE. Domain sequence information can be added to the file by using
           DOMAINSEQS.

       -datafile matrixf
           This option specifies the secondary structure substitution matrix. Default value:
           SSSUB

   Required section
       -maxhits integer
           This option specifies the number of top-scoring matches to report. Default value: 5

   Additional section
       -rgapopen float
           This options specifies the gap insertion penalty for reside-based alignment. The gap
           insertion penalty is the score taken away when a gap is created. The best value
           depends on the choice of comparison matrix. The default value assumes you are using
           the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide
           sequences. Default value: 10

       -rgapextend float
           This options specifies the gap extension penalty for residue-based alignment. The gap
           extension, penalty is added to the standard gap penalty for each base or residue in
           the gap. This is how long gaps are penalized. Usually you will expect a few long gaps
           rather than many short gaps, so the gap extension penalty should be lower than the gap
           penalty. Default value: 0.5

       -egapopen float
           This options specifies the gap insertion penalty for element-based alignment. The gap
           insertion penalty is the score taken away when a gap is created. The best value
           depends on the choice of comparison matrix. The default value assumes you are using
           the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide
           sequences. Default value: 10

       -egapextend float
           This options specifies the gap extension penalty for secondary structure element-based
           alignment. The gap extension, penalty is added to the standard gap penalty for each
           base or residue in the gap. This is how long gaps are penalized. Usually you will
           expect a few long gaps rather than many short gaps, so the gap extension penalty
           should be lower than the gap penalty. Default value: 0.5

   Output section
       -outssfile outfile
           This option specifies the name of the file containing top-scoring domains for
           residue-based alignment (output).A 'domain classification file' contains
           classification and other data for domains from SCOP or CATH, in DCF format
           (EMBL-like).

       -outsefile outfile
           This option specifies the name of the file containing top-scoring domains for
           secondary structure element-based alignment (output). A 'domain classification file'
           contains classification and other data for domains from SCOP or CATH, in DCF format
           (EMBL-like).

       -logfile outfile
           This option specifies the name of the ssematch log file (output). Default value:
           ssematch.log

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or
       directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       ssematch is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package.
       It can be redistributed under the same terms as EMBOSS itself.