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.