NAME
Bio::GeneDesign::Basic
VERSION
Version 5.56
DESCRIPTION
GeneDesign is a library for the computer-assisted design of synthetic genes
AUTHOR
Sarah Richardson <SMRichardson@lbl.gov>
Definitions
Functions
_generate_dimers
_sanitize()
remove non nucleotide characters from nucleotide sequences. remove non amino acid characters from peptide sequences. return sanitized strand and list of bad characters.
_count()
takes a nucleotide sequence and returns a base count. Looks for total length, purines, pyrimidines, and degenerate bases. If degenerate bases are present assumes their substitution for non degenerate bases is totally random for percentage estimation.
in: nucleotide sequence (string),
out: base count (hash)_gcwindows()
takes a nucleotide sequence, a window size, and minimum and maximum values. returns lists of real coordinates of subsequences that violate mimimum or maximum GC percentages.
Values are returned inside an array reference such that the first value is an array ref of minimum violators (as array refs of left/right coordinates), and the second value is an array ref of maximum violators.
$return_value = [ [[left, right], [left, right]], #minimum violators [[left, right], [left, right]] #maximum violators ];
_melt()
takes a nucleotide sequence and returns a melting temperature
in: nucleotide sequence (string)
salt concentration (string, opt, def =.05),
oligo concentration (string, opt, def = .0000001)
out: temperature (float)_ntherm()
takes a nucleotide sequence and returns a nearest neighbor melting temp.
in: nucleotide sequence (string)
out: temperature (float)_complement()
takes a nucleotide sequence and returns its complement or reverse complement.
in: nucleotide sequence (string),
switch for reverse complement (1 or null)
out: nucleotide sequence (string)_toRNA()
_regres()
takes a sequence that may be degenerate and returns a string that is prepped for use in a regular expression.
in: sequence (string),
switch for aa or nt sequence (1 or null)
out: regexp string (string)regarr()
_positions()
_find_runs
_is_ambiguous
_compare_sequences()
takes two nucleotide sequences that are assumed to be perfectly aligned and roughly equivalent and returns similarity metrics. should be twweeaakkeedd
in: 2x nucleotide sequence (string)
out: similarity metrics (hash)_amb_transcription
_add_arr
Basically builds a list of tree nodes for the amb_trans* functions. in: 2 x peptide lists (array reference) out: combined list of peptides
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.