NAME

       seqfraggle - Removes fragment sequences from DHF files.

SYNOPSIS

       seqfraggle -dhfinpath dirlist -thresh integer -dhfoutdir outdir

       seqfraggle -help

DESCRIPTION

       seqfraggle 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
       -dhfinpath dirlist
           This option specifies the location of DHF files (domain hits files) or other sequence
           files (input). A 'domain hits file' contains database hits (sequences) with domain
           classification information, in FASTA or EMBL formats. 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. Alternatively, SEQFRAGGLE
           will accept sequence or sequence sets in any of the common formats. Default value: ./

   Required section
       -thresh integer
           This option specifies the percentage of median length for definition of fragments.
           SEQFRAGGLE first determines the median length of all the sequences in the input file,
           then discards any hit sequences which are not within a threshold percentage of the
           median length. The remaining sequences are written to the output file. Default value:
           50

   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 or EMBL formats. 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. Alternatively, SEQFRAGGLE will write output
           files in any of the common formats. Default value: ./

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

       seqfraggle 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.