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 listThis 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 listThis option specifies which alignment
algorithm to use. Default value: 1
Additional section¶
-forcetype booleanThis 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 outdirThis 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.08/11/2010 | DOMALIGN 0.1.0+20100721 |