ssematch - Search a DCF file for secondary structure matches.
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
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).
-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
-maxhits integer
This option specifies the number of top-scoring matches
to report. Default value: 5
-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
-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 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).
ssematch is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.