This is the command domainseqse 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
domainseqs - Adds sequence records to a DCF file.
SYNOPSIS
domainseqs -dcfinfile infile -dpdbdir directory -getswiss toggle -pdbtospfile infile
-datafile matrixf -gapopen float -gapextend float -dcfoutfile outfile
-logfile outfile
domainseqs -help
DESCRIPTION
domainseqs 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
-dcfinfile infile
This option specifies the name of 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.
-dpdbdir directory
This option specifies the location of domain CCF file (clean coordinate files)
(input). A 'clean cordinate file' contains coordinate and other data for a single PDB
file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files,
generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up'
data that is self-consistent and error-corrected. Records for residue solvent
accessibility and secondary structure are added to the file by using PDBPLUS. Default
value: ./
-getswiss toggle
Default value: N
-pdbtospfile infile
This option specifies the name of the pdbcodes to swissprot indexing file. The
swissprot:PDB equivalence file is generated by PDBTOSP
-datafile matrixf
This option specifies the residue substitution matrix, which is used for sequence
comparison. Default value: EBLOSUM62
Required section
Additional section
-gapopen float
This option specifies the gap insertion penalty. This 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
-gapextend float
This option specifies the gap extension penalty. This 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
-dcfoutfile outfile
This option specifies the name of DCF file (domain classification file) (output). 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. Default value: domainseqs.out
-logfile outfile
This option specifies the name of log file for the build. The log file contains
messages about any errors arising while domainseqs ran. Default value: domainseqs.log
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