Provided by: emboss_6.6.0+dfsg-7_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.

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.