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ssematch
Langue: en
Version: 09/25/2007 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
ssematch - Search a DCF file for secondary structure matches.SYNOPSIS
- ssematch -ssinfile infile -dcfinfile infile [-datafile matrixf] -maxhits integer [-gapopenr float] [-gapextendr float] [-gapopene float] [-gapextende 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
-gapopenr 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
-gapextendr 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
-gapopene 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
-gapextende 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 alinnment (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 alinnment (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 EMBOSS Packaging Team <pkg-emboss-devel@lists.alioth.debian.org>
- Wrote the script used to autogenerate this manual page.
COPYRIGHT
Copyright © 2007 Debian EMBOSS Packaging TeamThis manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre