/usr/share/EMBOSS/acd/ssematch.acd is in embassy-domainatrix 0.1.0+20100721-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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documentation: "Search a DCF file for secondary structure
matches."
groups: "Utils:Database creation"
gui: "yes"
batch: "yes"
cpu: "medium"
embassy: "domainatrix"
]
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: Free text file"
]
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: Free text file"
]
matrixf: datafile [
additional: "Y"
information: "Residue substitution matrix"
help: "This option specifies the secondary structure substitution
matrix."
default: "SSSUB"
relations: "EDAM: Float comparison matrix"
]
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: Generic integer"
]
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: Generic float"
]
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: Generic float"
]
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: Generic float"
]
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: Generic float"
]
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: EMBASSY domain classification record"
]
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: EMBASSY domain classification record"
]
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: Domainatrix log file"
]
endsection: output
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