This is the command seqsorte that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
seqsort - Remove ambiguous classified sequences from DHF files.
SYNOPSIS
seqsort -dhfindir directory -overlap integer -dofamilies toggle -doambiguities toggle
-dhfoutdir outdir -hitsfile outfile -ambigfile outfile
seqsort -help
DESCRIPTION
seqsort 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
-dhfindir directory
This option specifies the location of DHF files (domain hits files) (input). A 'domain
hits file' contains database hits (sequences) with domain classification information,
in the DHF format (FASTA or EMBL-like). 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. Default value: ./
Required section
-overlap integer
This option specifies the number of overlapping residues required for merging of two
hits. Each family is also processed so that ovlerapping hits (hits with identical
accesssion number that overlap by at least a user-defined number of residues) are
replaced by a hit that is produced from merging the two overlapping hits. Default
value: 10
-dofamilies toggle
This option specifies to write a domain families file. If this option is set a domain
families file is written. Default value: N
-doambiguities toggle
This option specifies whether to write a domain ambiguities file. If this option is
set a domain ambiguities file is written. Default value: N
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 the DHF format (FASTA or EMBL-like). 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. Default value: ./
-hitsfile outfile
This option specifies the name of domain families file (output). A 'domain families
file' contains sequence relatives (hits) for each of a number of different SCOP or
CATH families found from searching a sequence database, e.g. by using SEQSEARCH
(psiblast). The file contains the collated search results for the indvidual families;
only those hits of unambiguous family assignment are included. Hits of ambiguous
family assignment are assigned as relatives to a SCOP or CATH superfamily or fold
instead and are collated into a 'domain ambiguities file'. The domain families and
ambiguities files are generated by using SEQSORT and use the same format as a DHF file
(domain hits file). Default value: fam.dhf
-ambigfile outfile
This option specifies the name of domain ambiguities file (output). A 'domain families
file' contains sequence relatives (hits) for each of a number of different SCOP or
CATH families found from searching a sequence database, e.g. by using SEQSEARCH
(psiblast). The file contains the collated search results for the indvidual families;
only those hits of unambiguous family assignment are included. Hits of ambiguous
family assignment are assigned as relatives to a SCOP or CATH superfamily or fold
instead and are collated into a 'domain ambiguities file'. The domain families and
ambiguities files are generated by using SEQSORT and use the same format as a DHF file
(domain hits file). Default value: oth.dhf
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