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Bio-GeneDesign-5.56
River stage zero No dependents
++
/ Bio::GeneDesign::Random

NAME

GeneDesign::Random

VERSION

Version 5.56

DESCRIPTION

Random DNA Generators

AUTHOR

Sarah Richardson <SMRichardson@lbl.gov>

Functions

_randomDNA()

  takes a target length and a GC percentage and generates a random nucleotide
  sequence, with or without stops in the first frame
  in: nucleotide sequence length (scalar),
      GC percentage (0 <= scalar <= 100),
      stop codon prevention(0 stops allowed, else no stops),
      codon table (hash reference)
  out: nucleotide sequence (string)

_randombase()

  when you just want one random base

_random_weighted_base()

  when you just want one random but weighted base

_weighted_rand()

_replace_ambiguous_bases

_random_index

COPYRIGHT AND LICENSE

Copyright (c) 2015, Sarah Richardson All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

* The names of Johns Hopkins, the Joint Genome Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the GeneDesign developers may not be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.