bionic (1) skipredundant.1e.gz

Provided by: emboss_6.6.0+dfsg-6build1_amd64 bug

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


BUGS
       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to
       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).


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.


       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.