ssematch - Search a DCF file for secondary structure matches.

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

       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).

       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.

DOMAINATRIX 0.1.0+20100721                         08/11/2010                                       SSEMATCH(1e)

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).

       ssematch - Search a DCF file for secondary structure matches.

Inputsection-ssinfileinfile
           This option specifies the name of the file of secondary structure (input).

       -dcfinfileinfile
           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.

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

   Requiredsection-maxhitsinteger
           This option specifies the number of top-scoring matches to report. Default value: 5

   Additionalsection-rgapopenfloat
           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

       -rgapextendfloat
           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

       -egapopenfloat
           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

       -egapextendfloat
           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

   Outputsection-outssfileoutfile
           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).

       -outsefileoutfile
           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).

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

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

ssematch-ssinfileinfile-dcfinfileinfile [-datafilematrixf] -maxhitsinteger [-rgapopenfloat]
                [-rgapextendfloat] [-egapopenfloat] [-egapextendfloat] -outssfileoutfile-outsefileoutfile-logfileoutfilessematch-help