seqfraggle1e
Removes fragment sequences from dhf files.
Usage
seqfraggle -dhfinpath
dirlist
-thresh
integer
-dhfoutdir
outdir
seqfraggle -help
Overview
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: ./
Releases
Unchanged in 7 releases since Debian 7 (Wheezy).