SEQSORT(1e)
NAME
seqsort - Remove ambiguous classified sequences from DHF files.
SYNOPSIS
seqsort -dhfindir directory -overlap integer -dofamilies toggle -doambiguities toggle -dhfoutdir outdir -hitsfile outfile -ambigfile outfile seqsort -help
DESCRIPTION
seqsort 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
- -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
- -overlap integer
This option specifies the number of overlapping residues required
for merging of two hits. Each family is also processed so that
ovlerapping hits (hits with identical accesssion number that
overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits.
Default value: 10 - -dofamilies toggle
This option specifies to write a domain families file. If this
option is set a domain families file is written. Default value: N - -doambiguities toggle
This option specifies whether to write a domain ambiguities file.
If this option is set a domain ambiguities file is written. Default value: N - 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 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: ./ - -hitsfile outfile
This option specifies the name of domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file
contains the collated search results for the indvidual families;
only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are
generated by using SEQSORT and use the same format as a DHF file
(domain hits file). Default value: fam.dhf - -ambigfile outfile
This option specifies the name of domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for
each of a number of different SCOP or CATH families found from
searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual
families; only those hits of unambiguous family assignment are
included. Hits of ambiguous family assignment are assigned as
relatives to a SCOP or CATH superfamily or fold instead and are
collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same
format as a DHF file (domain hits file). Default value: oth.dhf
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
seqsort 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.