SEQFRAGGLE(1e)						     EMBOSS Manual for Debian						    SEQFRAGGLE(1e)

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.

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