/usr/share/EMBOSS/acd/seqalign.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.
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documentation: "Extend alignments (DAF file) with sequences
(DHF file)."
groups: "Protein:Domains, Alignment:Local"
gui: "yes"
batch: "yes"
cpu: "high"
embassy: "domalign"
external: "clustalw"
relations: "EDAM_topic:0182 Sequence alignment"
relations: "EDAM_topic:0736 Protein domains and folds"
relations: "EDAM_operation:0292 Sequence alignment construction"
]
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_data:2527 Parameter"
]
dirlist: dhfinpath [
standard: "@($(mode)==1)"
information: "Program seqalign input directories"
help: "This option specifies the location of sequences, e.g. DHF
files (domain hits files) (input). SEQALIGN takes as input a
database of either i. single sequences, ii. sets of unaligned
sequences or iii. sets of aligned sequences, e.g. a domain
alignment file. A 'domain alignment file' contains a sequence
alignment of domains belonging to the same SCOP or CATH family.
The file is in clustal format annotated with domain family
classification information. The files generated by using SCOPALIGN
will contain a structure-based sequence alignment of domains of
known structure only. Such alignments can be extended with
sequence relatives (of unknown structure) by using SEQALIGN."
default: "./"
extension: "dhf"
knowntype: "seqalign input"
nullok: "Y"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:0849 Sequence record"
relations: "EDAM_format:1219 pure protein"
]
dirlist: dafinpath [
standard: "@($(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_identifier:1049 Directory name"
relations: "EDAM_data:1384 Sequence alignment (protein)"
]
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_identifier:1049 Directory name"
relations: "EDAM_data:0849 Sequence record"
relations: "EDAM_format:1219 pure protein"
]
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_identifier:1190 Tool name"
]
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_data:2527 Parameter"
]
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_identifier:1049 Directory name"
relations: "EDAM_data:1384 Sequence alignment (protein)"
]
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_data:1678 Tool log"
]
endsection: output
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