/usr/share/EMBOSS/acd/domainseqs.acd is in embassy-domainatrix 0.1.660-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 | application: domainseqs [
documentation: "Add sequence records to a DCF file."
groups: "Utils:Database creation, Protein:Domains"
gui: "yes"
batch: "yes"
cpu: "medium"
embassy: "domainatrix"
relations: "EDAM_topic:0091 Data handling"
relations: "EDAM_topic:0736 Protein domains and folds"
relations: "EDAM_operation:2234 Structure file processing"
]
section: input [
information: "Input section"
type: "page"
]
infile: dcfinfile [
parameter: "Y"
information: "Domain classification file"
help: "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."
knowntype: "domain classification"
relations: "EDAM_data:0900 Protein domain classification"
]
directory: dpdbdir [
parameter: "Y"
information: "Clean domain coordinates directory"
help: "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: "./"
extension: "ccf"
knowntype: "domain clean coordinates"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:1468 Protein domain"
]
toggle: getswiss [
standard: "Y"
information: "Retrieve swissprot sequence."
default: "N"
relations: "EDAM_data:2527 Parameter"
]
infile: pdbtospfile [
standard: "$(getswiss)"
information: "Swissprot:pdb equivalence table file
(optional)"
help: "This option specifies the name of the pdbcodes to swissprot
indexing file. The swissprot:PDB equivalence file is generated by
PDBTOSP"
knowntype: "swissprot pdb equivalence table"
nullok: "Y"
relations: "EDAM_data:0954 Database cross-mapping"
]
matrixf: datafile [
additional: "$(getswiss)"
information: "Residue substitution matrix."
help: "This option specifies the residue substitution matrix,
which is used for sequence comparison."
default: "EBLOSUM62"
relations: "EDAM_data:1449 Comparison matrix (amino acid)"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
endsection: required
section: additional [
information: "Additional section"
type: "page"
]
float: gapopen [
additional: "$(getswiss)"
information: "Gap insertion penalty."
minimum: "1."
maximum: "100."
default: "10"
valid: "Floating point number from 1.0 to 100.0"
expected: "10.0 for any sequence"
help: "This option specifies the gap insertion penalty. This is
the score taken away when a gap is created. The best value depends
on the choice of comparison matrix. The default value assumes you
are using the EBLOSUM62 matrix for protein sequences, and the
EDNAFULL matrix for nucleotide sequences."
relations: "EDAM_data:1397 Gap opening penalty"
]
float: gapextend [
additional: "$(getswiss)"
information: "Gap extension penalty."
minimum: "0.0"
maximum: "10."
default: "0.5"
valid: "Floating point number from 0.0 to 10.0"
expected: "0.5 for any sequence"
help: "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."
relations: "EDAM_data:1398 Gap extension penalty"
]
endsection: additional
section: output [
information: "Output section"
type: "page"
]
outfile: dcfoutfile [
parameter: "Y"
information: "Domain classification output file"
help: "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: "domainseqs.out"
knowntype: "domain classification"
relations: "EDAM_data:0900 Protein domain classification"
]
outfile: logfile [
standard: "Y"
information: "Domainatrix log output file"
help: "This option specifies the name of log file for the build.
The log file contains messages about any errors arising while
domainseqs ran."
default: "domainseqs.log"
knowntype: "domainatrix log"
relations: "EDAM_data:1678 Tool log"
]
endsection: output
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