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seqfraggle.1e.gz

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)
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