DOMAINSEQS(1e) | EMBOSS Manual for Debian | DOMAINSEQS(1e) |
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 infileThis 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 floatThis 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 outfileThis 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
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¶
domainseqs is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this
manual page.
COPYRIGHT¶
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.08/11/2010 | DOMAINATRIX 0.1.0+20100721 |