NAME¶
seqsearch - Generate PSI-BLAST hits (DHF file) from a DAF
file.
SYNOPSIS¶
seqsearch -mode list
-inseqspath dirlist
-database string
-niter integer
-evalue float
-maxhits integer
-dhfoutdir outdir
-logfile outfile
seqsearch -help
DESCRIPTION¶
seqsearch 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¶
-mode list
This option specifies the mode of SEQSEARCH operation.
SEQSEARCH 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
-inseqspath dirlist
This option specifies the location of sequences, e.g. DAF
files (domain alignment files) (input). SEQSEARCH 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: ./
-database string
Default value: swissprot
Required section¶
-niter integer
This option specifies the number of PSIBLAST iterations.
This option specifies the number of PSIBLAST iterations that are performed in
a search. Default value: 1
-evalue float
This option specifies the threshold E-value for inclusion
in family. This option specifies the threshold E-value for a PSIBLAST hit to
be retained. Default value: 0.001
-maxhits integer
This option specifies the maximum number of hits. This
option specifies the maximum number of PSIBLAST hit that are retained. It
should normally be set high so that nothing is discarded. Default value:
1000
Output section¶
-dhfoutdir outdir
This option specifies the location of DHF files (domain
hits files) (output). A 'domain hits file' contains database hits (sequences)
with domain classification information, in FASTA format. 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: ./
-logfile outfile
This option specifies the name of log file for the build.
The log file contains messages about any errors arising while SEQSEARCH ran.
Default value: seqsearch.log
SEE ALSO¶
seqsearch 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.
