/usr/share/EMBOSS/acd/ssematch.acd is in embassy-domainatrix 0.1.650-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 | application: ssematch [
documentation: "Search a DCF file for secondary structure
matches."
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:0500 Secondary structure alignment construction"
]
section: input [
information: "Input section"
type: "page"
]
infile: ssinfile [
parameter: "Y"
information: "Secondary structure file"
help: "This option specifies the name of the file of secondary
structure (input)."
knowntype: "Secondary structure"
relations: "EDAM_data:0876 Protein features (secondary structure)"
]
infile: dcfinfile [
parameter: "Y"
information: "Domain classification file"
help: "This option specifies the name of the 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"
]
matrixf: datafile [
additional: "Y"
information: "Residue substitution matrix"
help: "This option specifies the secondary structure substitution
matrix."
default: "SSSUB"
relations: "EDAM_data:1449 Comparison matrix (amino acid)"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
integer: maxhits [
standard: "Y"
information: "Number of top-scoring matches to report."
help: "This option specifies the number of top-scoring matches to
report."
default: "5"
relations: "EDAM_data:1694 Number of output entities"
]
endsection: required
section: additional [
information: "Additional section"
type: "page"
]
float: rgapopen [
additional: "Y"
information: "Gap insertion penalty for reside-based
alignment"
minimum: "1."
maximum: "100."
default: "10"
valid: "Floating point number from 1.0 to 100.0"
expected: "10.0 for any sequence"
help: "This options specifies the gap insertion penalty for
reside-based alignment. The gap insertion penalty 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: rgapextend [
additional: "Y"
information: "Gap extension penalty for residue-based
alignment"
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 options specifies the gap extension penalty for
residue-based alignment. The gap extension, penalty 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"
]
float: egapopen [
additional: "Y"
information: "Gap insertion penalty for secondary structure
element-based alignment."
minimum: "1."
maximum: "100."
default: "10"
valid: "Floating point number from 1.0 to 100.0"
expected: "10.0 for any sequence"
help: "This options specifies the gap insertion penalty for
element-based alignment. The gap insertion penalty 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: egapextend [
additional: "Y"
information: "Gap extension penalty for secondary structure
element-based alignment"
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 options specifies the gap extension penalty for
secondary structure element-based alignment. The gap extension,
penalty 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: outssfile [
parameter: "Y"
information: "Domain classification residue-based output
file"
help: "This option specifies the name of the file containing
top-scoring domains for residue-based alignment (output).A 'domain
classification file' contains classification and other data for
domains from SCOP or CATH, in DCF format (EMBL-like)."
knowntype: "domain classification"
relations: "EDAM_data:0900 Protein domain classification"
]
outfile: outsefile [
parameter: "Y"
information: "Domain classification structure-based output
file"
help: "This option specifies the name of the file containing
top-scoring domains for secondary structure element-based
alignment (output). A 'domain classification file' contains
classification and other data for domains from SCOP or CATH, in
DCF format (EMBL-like)."
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 the ssematch log file
(output)."
default: "ssematch.log"
knowntype: "domainatrix log"
relations: "EDAM_data:1678 Tool log"
]
endsection: output
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