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 dirlistThis 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 integerThis 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 outdirThis 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.08/11/2010 | DOMSEARCH 0.1.0++20100721 |