This is the command skipredundante 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
skipredundant - Remove redundant sequences from an input set
SYNOPSIS
skipredundant -feature toggle -sequences seqset [-datafile matrixf] -mode list
-threshold float -minthreshold float -maxthreshold float -gapopen float
-gapextend float -outseq seqoutall -redundantoutseq seqoutall
skipredundant -help
DESCRIPTION
skipredundant is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Edit" command group(s).
OPTIONS
Input section
-feature toggle
Sequence feature information will be retained if this option is set.
-sequences seqset
-datafile matrixf
This is the scoring matrix file used when comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of the EMBOSS installation.
Required section
-mode list
This option specifies whether to remove redundancy at a single threshold percentage
sequence similarity or remove redundancy outside a range of acceptable threshold
percentage 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
-threshold float
This option specifies the percentage sequence identity redundancy threshold. The
percentage 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
-minthreshold float
This option specifies the percentage sequence identity redundancy threshold (lower
limit). The percentage 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
-maxthreshold float
This option specifies the percentage sequence identity redundancy threshold (upper
limit). The percentage 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
-gapopen float
The gap open 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: @($(acdprotein)? 10.0 : 10.0 )
-gapextend float
The gap extension, penalty is added to the standard gap penalty for each base or
residue in the gap. This is how long gaps are penalized. Usually you will expect a few
long gaps rather than many short gaps, so the gap extension penalty should be lower
than the gap penalty. An exception is where one or both sequences are single reads
with possible sequencing errors in which case you would expect many single base gaps.
You can get this result by setting the gap open penalty to zero (or very low) and
using the gap extension penalty to control gap scoring. Default value:
@($(acdprotein)? 0.5 : 0.5 )
Advanced section
Output section
-outseq seqoutall
-redundantoutseq seqoutall
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