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¶
-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 )
Output section¶
-outseq seqoutall
-redundantoutseq seqoutall
SEE ALSO¶
skipredundant is fully documented via the tfm(1)
system.
AUTHOR¶
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition
of the EMBOSS package. It can be redistributed under the same terms as
EMBOSS itself.
