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skipredundant(1e)


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.



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