seqfraggle - Removes fragment sequences from DHF files.
seqfraggle
-dhfinpath dirlist
-thresh integer
-dhfoutdir outdir
seqfraggle -help
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).
-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:
./
-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
-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 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).
seqfraggle is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.