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CONTENTS
1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES
1.0 SUMMARY
Add sequence records to a DCF file
2.0 INPUTS & OUTPUTS
DOMAINSEQS parses a DCF file (domain classification file) and writes a
file containing the same data, except that domain sequence information
derived from structural and, optionally, sequence databases are added.
Domain sequences are taken from domain CCF files (clean coordinate
files) and (optionally) the swissprot database. If the swissprot
sequence is used, DOMAINSEQS requires a swissprot:PDB equivalence file
that gives the accession number of each PDB file corresponding to the
domains in the DCF file. The path for the CCF files (input) and names
of DCF files (input and output) are specified by the user. A log file
is also written.
3.0 INPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Input files for usage example
File: ../scopparse-keep/all.scop
ID D1CS4A_
XX
EN 1CS4
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Adenylyl cyclase VC1, domain C1a
XX
OS Dog (Canis familiaris)
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
ID D1II7A_
XX
EN 1II7
XX
TY SCOP
XX
SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Metallo-dependent phosphatases
XX
SF Metallo-dependent phosphatases
XX
FA DNA double-strand break repair nuclease
XX
DO Mre11
XX
OS Archaeon Pyrococcus furiosus
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
File: ../pdbtosp-domainatrix/Epdbtosp.dat
EN 101M
XX
NE 1
XX
IN MYG_PHYCA ID; P02185 ACC;
XX
//
EN 102L
XX
NE 1
XX
IN LYCV_BPT4 ID; P00720 ACC;
XX
//
EN 102M
XX
NE 1
XX
IN MYG_PHYCA ID; P02185 ACC;
XX
//
EN 103L
XX
NE 1
XX
IN LYCV_BPT4 ID; P00720 ACC;
XX
//
EN 103M
XX
NE 1
XX
IN MYG_PHYCA ID; P02185 ACC;
XX
//
EN 9XIA
XX
NE 1
XX
IN XYLA_STRRU ID; P24300 ACC;
XX
//
EN 9XIM
XX
NE 1
XX
IN XYLA_ACTMI ID; P12851 ACC;
XX
//
4.0 OUTPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
DOMAINSEQS may add the following records:
* (1) AC - Accession number of the domain sequence. This record will
only be present if the DCF file has been processed using DOMAINSEQS
and if an accession number for the PDB file corresponding to the
domain is given in the swissprot:PDB equivalence file (generated by
PDBTOSP) that DOMAINSEQS makes use of.
* (2) SP - Swissprot code of the domain sequence. This record will
only be present if the domain classification file has been
processed using DOMAINSEQS and if an swissprot code for the PDB
file corresponding to the domain is given in the swissprot:PDB
equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use
of.
* (3) RA - Position of domain in swissprot sequence. The integers
preceeding START and END give the start and end points respectively
of the domain sequence relative to the full-length swissprot
sequence.
* (4) SQ - Sequence of the domain according to swissprot. This
sequence is taken from the swissprot database. The SQ record will
only be present if the SCOP classification file has been processed
using DOMAINSEQS and if an accession number for the PDB file
corresponding to the domain is given in the swissprot:PDB
equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use
of.
Output files for usage example
File: all_s.scop
ID D1CS4A_
XX
EN 1CS4
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Adenylyl cyclase VC1, domain C1a
XX
OS Dog (Canis familiaris)
XX
DS SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64;
ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
ID D1II7A_
XX
EN 1II7
XX
TY SCOP
XX
SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Metallo-dependent phosphatases
XX
SF Metallo-dependent phosphatases
XX
FA DNA double-strand break repair nuclease
XX
DO Mre11
XX
OS Archaeon Pyrococcus furiosus
XX
DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;
MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
LKKAI
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
File: domainseqs.log
//
D1CS4A_
NO_ACCESSION_NUMBER
//
D1II7A_
NO_ACCESSION_NUMBER
5.0 DATA FILES
If the user specified retrieval of sequences from a sequence database,
DOMAINSEQS uses a swissprot:PDB equivalence file is generated by using
PDBTOSP.
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
Add sequence records to a DCF file.
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-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.
-getswiss toggle [N] Retrieve swissprot sequence.
* -pdbtospfile infile This option specifies the name of the
pdbcodes to swissprot indexing file. The
swissprot:PDB equivalence file is generated
by PDBTOSP
[-dcfoutfile] outfile [domainseqs.out] 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.
-logfile outfile [domainseqs.log] This option specifies the
name of log file for the build. The log file
contains messages about any errors arising
while domainseqs ran.
Additional (Optional) qualifiers (* if not always prompted):
* -datafile matrixf [EBLOSUM62] This option specifies the
residue substitution matrix, which is used
for sequence comparison.
* -gapopen float [10.0 for any sequence] 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. (Floating point
number from 1.0 to 100.0)
* -gapextend float [0.5 for any sequence] 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. (Floating point number
from 0.0 to 10.0)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dpdbdir" associated qualifiers
-extension2 string Default file extension
"-dcfoutfile" associated qualifiers
-odirectory3 string Output directory
"-logfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
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