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DOMAINSEQS documentation |
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; // |
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 // |
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;
//
|
// D1CS4A_ NO_ACCESSION_NUMBER // D1II7A_ NO_ACCESSION_NUMBER |
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:
"-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. 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
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-dcfinfile] (Parameter 1) |
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. | Input file | Required |
| [-dpdbdir] (Parameter 2) |
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. | Directory | ./ |
| -getswiss | Retrieve swissprot sequence. | Toggle value Yes/No | No |
| -pdbtospfile | This option specifies the name of the pdbcodes to swissprot indexing file. The swissprot:PDB equivalence file is generated by PDBTOSP | Input file | Required |
| [-dcfoutfile] (Parameter 3) |
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. | Output file | domainseqs.out |
| -logfile | This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainseqs ran. | Output file | domainseqs.log |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -datafile | This option specifies the residue substitution matrix, which is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62 |
| -gapopen | 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 | 10.0 for any sequence |
| -gapextend | 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 | 0.5 for any sequence |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
% domainseqs Adds sequence records to a DCF file. Domain classification file: ../scopparse-keep/all.scop Clean domain coordinates directory [./]: ../domainer-keep Retrieve swissprot sequence. [N]: Y Swissprot:pdb equivalence table file (optional): ../pdbtosp-keep/Epdbtosp.dat Domain classification output file [domainseqs.out]: all_s.scop Domainatrix log output file [domainseqs.log]: // D1CS4A_ // D1II7A_ |
Go to the input files for this example
Go to the output files for this example
D1
(A) XXXXXXXXXXXXXXXXXXXXX
D1 D2 D1
(B) XXXXXXXXXX-----------XXXXXXXXXXX
It should be clear that for an alignment retrieving B, the start and end
points for the retrieved sequence would be misleading.
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from SCOP. | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
| Domain classification file (for CATH) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
| Clean coordinate file (for protein) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. | PDBPARSE | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
| Clean coordinate file (for domain) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
| swissprot:PDB equivalence file | EMBL-like format. | A file containing swissprot identifiers for PDB codes. | Included in the EMBOSS distribution | N.A. |
| Program name | Description |
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX |
| allversusall | Sequence similarity data from all-versus-all comparison |
| cathparse | Generates DCF file from raw CATH files |
| cutgextract | Extract codon usage tables from from CUTG database |
| domainer | Generates domain CCF files from protein CCF files |
| domainnr | Removes redundant domains from a DCF file |
| domainsse | Add secondary structure records to a DCF file |
| hetparse | Converts heterogen group dictionary to EMBL-like format |
| jaspextract | Extract data from JASPAR |
| pdbparse | Parses PDB files and writes protein CCF files |
| pdbplus | Add accessibility & secondary structure to a CCF file |
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
| printsextract | Extract data from PRINTS database for use by pscan |
| prosextract | Processes the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| scopparse | Generate DCF file from raw SCOP files |
| seqnr | Removes redundancy from DHF files |
| sites | Generate residue-ligand CON files from CCF files |
| ssematch | Search a DCF file for secondary structure matches |
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |
See also http://emboss.sourceforge.net/