/usr/share/EMBOSS/acd/allversusall.acd is in embassy-domalign 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 | application: allversusall [
documentation: "Sequence similarity data from
all-versus-all comparison."
groups: "Utils:Database creation"
gui: "yes"
batch: "yes"
cpu: "medium"
embassy: "domalign"
relations: "EDAM_topic:0091 Data handling"
relations: "EDAM_topic:0182 Sequence alignment"
relations: "EDAM_operation:0292 Sequence alignment construction"
relations: "EDAM_operation:0289 Sequence distance matrix generation"
]
section: input [
information: "Input section"
type: "page"
]
dirlist: seqinpath [
parameter: "Y"
default: "./"
extension: "fasta"
information: "Sequence directories"
knowntype: "protein sequence"
relations: "EDAM_data:2886 Sequence record (protein)"
]
matrixf: matrix [
additional: "Y"
information: "Residue substitution matrix"
help: "This option specifies the residue substitution matrix that
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: "Y"
information: "Gap insertion penalty"
minimum: "1.0"
maximum: "100.0"
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. 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: gapextend [
additional: "Y"
information: "Gap extension penalty"
minimum: "0.0"
maximum: "10.0"
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. 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. 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."
relations: "EDAM_data:1398 Gap extension penalty"
]
endsection: additional
section: output [
information: "Output section"
type: "page"
]
outdir: datoutdir [
parameter: "Y"
information: "Location of sequence similarity data files
(output)"
help: "This option specifies the location of sequence similarity
data files (output)."
default: "./"
extension: "out"
knowntype: "allversusall output"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:1413 Sequence similarity"
]
outfile: logfile [
standard: "Y"
information: "Domainatrix log output file"
default: "allversusall.log"
help: "This option specifies the name of ALLVERSUSALL log file
(output). The log file contains messages about any errors arising
while ALLVERSUSALL ran."
knowntype: "domainatrix log"
relations: "EDAM_data:1678 Tool log"
]
endsection: output
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