seqfraggle - Removes fragment sequences from DHF files.

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

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).

       seqfraggle - Removes fragment sequences from DHF files.

Inputsection-dhfinpathdirlist
           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: ./

   Requiredsection-threshinteger
           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

   Outputsection-dhfoutdiroutdir
           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: ./

       seqfraggle is fully documented via the tfm(1) system.

seqfraggle-dhfinpathdirlist-threshinteger-dhfoutdiroutdirseqfraggle-help