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DOMAINSEQS documentation |
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 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 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. -errfile outfile 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 This option specifies the residue substitution matrix, which is used for sequence comparison. * -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. * -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. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dcfoutfile" associated qualifiers -odirectory3 string Output directory "-errfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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 deaths
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 |
-errfile | 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. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence |
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
D1 (A) XXXXXXXXXXXXXXXXXXXXX D1 D2 D1 (B) XXXXXXXXXX-----------XXXXXXXXXXXIt 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 data from AAINDEX |
allversusall | Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values |
cathparse | Reads raw CATH classification files and writes DCF file (domain classification file) |
cutgextract | Extract data from CUTG |
domainer | Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file) |
domainnr | Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS |
domainsse | Adds secondary structure records to a DCF file (domain classification file) |
hetparse | Converts raw dictionary of heterogen groups to a file in EMBL-like format |
pdbparse | Parses PDB files and writes CCF files (clean coordinate files) for proteins |
pdbplus | Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain |
pdbtosp | Convert raw swissprot:PDB equivalence file to EMBL-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scopparse | Reads raw SCOP classification files and writes a DCF file (domain classification file) |
seqnr | Removes redundancy from DHF files (domain hits files) or other files of sequences |
sites | Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file) |
ssematch | Searches a DCF file (domain classification file) for secondary structure matches |
tfextract | Extract data from TRANSFAC |
See also http://emboss.sourceforge.net/