This is the command seqnre 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
seqnr - Removes redundancy from DHF files.
SYNOPSIS
seqnr -dhfinpath dirlist -dosing toggle -singletsdir directory -dosets toggle
-insetsdir directory [-matrix matrixf] -mode list -thresh float -threshlow float
-threshup float [-gapopen float] [-gapextend float] -dhfoutdir outdir -dored toggle
-redoutdir outdir -logfile outfile
seqnr -help
DESCRIPTION
seqnr is a command line program from EMBOSS (“the European Molecular Biology Open Software
Suite”). It is part of the "Utils:Database creation" command group(s).
OPTIONS
Input section
-dhfinpath dirlist
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: ./
-dosing toggle
This option specifies whether to use singlet sequences (e.g. DHF files) to filter
input. Optionally, up to two further directories of sequences may be read: these are
considered in the redundancy calculation but never appear in the output files. Default
value: Y
-singletsdir directory
This option specifies the location of singlet filter sequences (e.g. DHF 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: ./
-dosets toggle
This option specifies whether to use sets of sequences (e.g. DHF files) to filter
input. Optionally, up to two further directories of sequences may be read: these are
considered in the redundancy calculation but never appear in the output files. Default
value: Y
-insetsdir directory
This option specifies location of sets of filter sequences (e.g. DAF files) (input). A
'domain alignment file' contains a sequence alignment of domains belonging to the same
SCOP or CATH family. The file is in clustal format annotated with domain family
classification information. The files generated by using SCOPALIGN will contain a
structure-based sequence alignment of domains of known structure only. Such alignments
can be extended with sequence relatives (of unknown structure) by using SEQALIGN.
Default value: ./
-matrix matrixf
This option specifies the residue substitution matrix that is used for sequence
comparison. Default value: EBLOSUM62
Required section
-mode list
This option specifies whether to remove redundancy at a single threshold % sequence
similarity or remove redundancy outside a range of acceptable threshold % similarity.
All permutations of pair-wise sequence alignments are calculated for each set of input
sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global
alignment algorithm. Redundant sequences are removed in one of two modes as follows:
(i) If a pair of proteins achieve greater than a threshold percentage sequence
similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair
of proteins have a percentage sequence similarity that lies outside an acceptable
range (specified by the user) the shortest sequence is discarded. Default value: 1
-thresh float
This option specifies the % sequence identity redundancy threshold. The % sequence
identity redundancy threshold determines the redundancy calculation. If a pair of
proteins achieve greater than this threshold the shortest sequence is discarded.
Default value: 95.0
-threshlow float
This option specifies the % sequence identity redundancy threshold (lower limit). The
% sequence identity redundancy threshold determines the redundancy calculation. If a
pair of proteins have a percentage sequence similarity that lies outside an acceptable
range the shortest sequence is discarded. Default value: 30.0
-threshup float
This option specifies the % sequence identity redundancy threshold (upper limit). The
% sequence identity redundancy threshold determines the redundancy calculation. If a
pair of proteins have a percentage sequence similarity that lies outside an acceptable
range the shortest sequence is discarded. Default value: 90.0
Additional section
-gapopen float
This option specifies the gap insertion penalty. The gap insertion penalty is the
score taken away when a gap is created. The best value depends on the choice of
comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for
protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: 10
-gapextend float
This option specifies the gap extension penalty. The gap extension, penalty is added
to the standard gap penalty for each base or residue in the gap. This is how long gaps
are penalized. Usually you will expect a few long gaps rather than many short gaps, so
the gap extension penalty should be lower than the gap penalty. Default value: 0.5
Output section
-dhfoutdir outdir
This option specifies the location of DHF files (domain hits files) of non-redundant
sequences (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: ./
-dored toggle
This option specifies whether to retain redundant sequences. If this option is set a
DHF file (domain hits file) of redundant sequences is written. Default value: N
-redoutdir outdir
This option specifies the location of DHF files (domain hits files) of redundant
sequences (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: ./
-logfile outfile
This option specifies the name of SEQNR log file (output). The log file contains
messages about any errors arising while SEQNR ran. Default value: seqnr.log
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