NAME

GeneDesign::RestictionEnzymes

VERSION

Version 3.00

DESCRIPTION

GeneDesign functions for handling restriction enzyme recognition sites

Functions

define_sites()

Generates a set of hash references containing information about the 
restriction enzyme library. All have the enzyme name as a key. 
  REGEX : ref to array containing regex-ready representations of enzyme 
          recognition site
  CLEAN : the recognition site as a string
  TABLE : the recognition site with cleavage annotation
  SCORE : usually the price
  TYPE  : whether the enzyme leaves 5', 3', or blunt ends, and whether or not 
          the enzyme leaves a 1bp overhang
  METHB : which methylation pattern blocks cleavage
  METHI : which methylation pattern inhibits cleavage
  STAR  : whether or not the enzyme has star activity
  TEMP  : optimal operating temperature for cleavage
  VEND  : which vendors supply the enzyme
in: enzyme list as a file path
out: hash of hash references

overhang()

define_site_status()

Generates a hash describing a restriction count of a nucleotide sequence.
in: nucleotide sequence as a string
    reference to a hash containing enzyme names as keys and regular
      expressions in a reference to an array as values
      (SITE_REGEX from define_sites)
out: reference to a hash where the keys are enzyme names and the value is a 
      count of their occurence in the nucleotide sequence

siteseeker()

Generates a hash describing the positions of a particular enzyme's recognition
sites in a nucleotide sequence.
in: nucleotide sequence as a string,
    an enzyme recognition site as a string, 
    reference to an array containing enzyme regular expressions
out: reference to a hash where the keys are positions and the value is the 
    recognition site from that position as a string.

filter_sites()

mutexclu()

first_base()

report_RE()

build_suffix_tree()

Builds two suffix trees from a list of restriction enzyme recognition sites
in: array of enzyme names,
    reference enzyme hash
out: array of suffix trees, one for forward orientaion, one for reverse

search_suffix_tree()

Working on a Bio::Seq::Feature::Store DB

search_DNA()

overhangP()

overhangA()

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

COPYRIGHT AND LICENSE

Copyright (c) 2011, GeneDesign developers 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. * Neither the name of the Johns Hopkins nor the names of the developers may 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.

cpanm Bio::GeneDesign::HTML

perl -MCPAN -e shell
install Bio::GeneDesign::HTML