This is the command ssematche that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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