SEQSORT(1e)						     EMBOSS Manual for Debian						       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.

DOMSEARCH 0.1.0++20100721					    08/11/2010							       SEQSORT(1e)