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¶
-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
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
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.