/usr/share/EMBOSS/acd/seqalign.acd is in embassy-domalign 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.
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 | application: seqalign [
documentation: "Extend alignments (DAF file) with sequences
(DHF file)."
groups: "Protein:3D Structure"
gui: "yes"
batch: "yes"
cpu: "high"
embassy: "domalign"
external: "clustalw"
]
section: input [
information: "Input section"
type: "page"
]
list: mode [
standard: "Y"
default: "1"
minimum: "1"
maximum: "1"
delimiter: ","
codedelimiter: ":"
values: "1: Single sequences, 2: Multiple sequences (e.g.
sequence set or alignment)"
header: "Input mode"
information: "Select mode of operation."
button: "Y"
help: "This option specifies the mode of SEQALIGN operation.
SEQALIGN takes as input a directory of either i. single sequences,
ii. set of sequences (unaligned or aligned, but typically aligned
sequences within a domain alignment file)). The user has to
specify which."
relations: "EDAM: Generic string array"
]
dirlist: dhfinpath [
standard: "@($(mode)==1)"
information: "Program seqalign input directories"
help: "This option specifies the location of sequences, e.g. DHF
files (domain hits files) (input). SEQALIGN takes as input a
database of either i. single sequences, ii. sets of unaligned
sequences or iii. sets of aligned sequences, e.g. a domain
alignment file. A 'domain alignment file' contains a sequence
alignment of domains belonging to the same SCOP or CATH family.
The file is in clustal format annotated with domain family
classification information. The files generated by using SCOPALIGN
will contain a structure-based sequence alignment of domains of
known structure only. Such alignments can be extended with
sequence relatives (of unknown structure) by using SEQALIGN."
default: "./"
extension: "dhf"
knowntype: "seqalign input"
nullok: "Y"
relations: "EDAM: EMBASSY domain hits report"
]
dirlist: dafinpath [
standard: "@($(mode)==2)"
information: "Domain alignment directories"
help: "This option specifies the location of sequences, e.g. DAF
files (domain alignment files) (input). SEQALIGN takes as input a
database of either i. single sequences, ii. sets of unaligned
sequences or iii. sets of aligned sequences, e.g. a domain
alignment file. A 'domain alignment file' contains a sequence
alignment of domains belonging to the same SCOP or CATH family.
The file is in clustal format annotated with domain family
classification information. The files generated by using SCOPALIGN
will contain a structure-based sequence alignment of domains of
known structure only. Such alignments can be extended with
sequence relatives (of unknown structure) by using SEQALIGN."
default: "./"
extension: "daf"
knowntype: "domain alignment"
nullok: "Y"
relations: "EDAM: EMBASSY domain alignment file"
]
directory: dhfindir [
parameter: "Y"
information: "Domain hits directory"
help: "This option specifies the location of DHF files (domain
hits files) (input). A 'domain hits file' contains database hits
(sequences) with domain classification information, in the DHF
format (FASTA or EMBL-like). The hits are relatives to a SCOP or
CATH family and are found from a search of a sequence database.
Files containing hits retrieved by PSIBLAST are generated by using
SEQSEARCH."
default: "./"
extension: "dhf"
knowntype: "domain hits"
relations: "EDAM: EMBASSY domain hits report"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
list: amode [
standard: "Y"
default: "1"
minimum: "1"
maximum: "1"
values: "1: CLUSTALW, 2: TCOFFEE (not yet implemented)"
help: "This option specifies which alignment algorithm to use."
delimiter: ","
codedelimiter: ":"
header: "Alignment algorithm option"
information: "Select number."
relations: "EDAM: Generic string array"
]
endsection: required
section: additional [
information: "Additional section"
type: "page"
]
boolean: forcetype [
additional: "Y"
information: "Force output of minimal domain classification
data."
help: "This option specifies whether to force minimal domain
classification data to be written to the output file in cases
where singlet sequences were given as input file and no
classification data was available"
default: "N"
relations: "EDAM: Generic boolean"
]
endsection: additional
section: output [
information: "Output section"
type: "page"
]
outdir: dafoutdir [
parameter: "Y"
information: "Domain alignment file output directory"
help: "This option specifies the location of DAF files (domain
alignment files) (output). A 'domain alignment file' contains a
sequence alignment of domains belonging to the same SCOP or CATH
family. The file is in clustal format annotated with domain family
classification information. The files generated by using
SCOPALIGN will contain a structure-based sequence alignment of
domains of known structure only. Such alignments can be extended
with sequence relatives (of unknown structure) by using SEQALIGN."
default: "./"
extension: "daf"
knowntype: "domain alignment"
relations: "EDAM: EMBASSY domain alignment file"
]
outfile: logfile [
standard: "Y"
information: "Domainatrix log output file"
default: "seqalign.log"
help: "This option specifies the name of log file for the build.
The log file contains messages about any errors arising while
SEQALIGN ran."
knowntype: "domainatrix log"
relations: "EDAM: Domainatrix log file"
]
endsection: output
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