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¶
-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
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.
