seqalign - Extend alignments (DAF file) with sequences (DHF
file).
seqalign -mode list
-dhfinpath dirlist
-dafinpath dirlist
-dhfindir directory
-amode list
[-forcetype boolean]
-dafoutdir outdir
-logfile outfile
seqalign -help
seqalign is a command line program from EMBOSS (“the
European Molecular Biology Open Software Suite”). It is part of the
"Protein:3D Structure" command group(s).
-mode list
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. Default value: 1
-dhfinpath dirlist
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 value: ./
-dafinpath dirlist
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 value: ./
-dhfindir directory
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 value: ./
-amode list
This option specifies which alignment algorithm to use.
Default value: 1
-forcetype boolean
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 value: N
-dafoutdir outdir
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
value: ./
-logfile outfile
This option specifies the name of log file for the build.
The log file contains messages about any errors arising while SEQALIGN ran.
Default value: seqalign.log
Bugs can be reported to the Debian Bug Tracking system
(http://bugs.debian.org/emboss), or directly to the EMBOSS developers
(http://sourceforge.net/tracker/?group_id=93650&atid=605031).
seqalign is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
This manual page was autogenerated from an Ajax Control Definition
of the EMBOSS package. It can be redistributed under the same terms as
EMBOSS itself.