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.