seqfragglee - Online in the Cloud

PROGRAM:

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: ./

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