SEQALIGN(1e) EMBOSS Manual for Debian SEQALIGN(1e)
NAME
seqalign - Extend alignments (DAF file) with sequences (DHF file).
SYNOPSIS
seqalign -mode list -dhfinpath dirlist -dafinpath dirlist -dhfindir directory -amode list [-forcetype boolean] -dafoutdir outdir
-logfile outfile
seqalign -help
DESCRIPTION
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).
OPTIONS
Input section
-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: ./
Required section
-amode list
This option specifies which alignment algorithm to use. Default value: 1
Additional section
-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
Output section
-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
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).
SEE ALSO
seqalign is fully documented via the tfm(1) system.
AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual page.
COPYRIGHT
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.
DOMALIGN 0.1.0+20100721 08/11/2010 SEQALIGN(1e)