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seqfraggle.1e

Langue: en

Version: 06/26/2010 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)

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.

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.

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