NAME
Bio::GeneDesign::RestrictionEnzymes
VERSION
Version 3.05
DESCRIPTION
GeneDesign functions for handling restriction enzymes
AUTHOR
Sarah Richardson <notadoctor@jhu.edu>
define_sites()
Generates a hash reference where the keys are enzyme names and the values are
Bio::GeneDesign::RestrictionEnzyme objects.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 sequencesiteseeker()
Generates a hash describing the positions of a particular enzyme's recognition
sites in a nucleotide sequence.
in: nucleotide sequence as a string,
Bio::GeneDesign::RestrictionEnzyme object
out: reference to a hash where the keys are positions and the value is the
recognition site from that position as a string.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
#NO UNIT TESTSsearch_suffix_trees()
#NO UNIT TESTSfirst_base
#NO UNIT TESTSoverhangP
#NO UNIT TESTSoverhangA
#NO UNIT TESTSfilter_by_stickiness
#NO UNIT TESTSfilter_by_cleavagesite
#NO UNIT TESTSfilter_by_overhangpalindromy
#NO UNIT TESTSfilter_by_length
#NO UNIT TESTSfilter_by_baseambiguity
#NO UNIT TESTSfilter_by_inactivationtemp
#NO UNIT TESTSfilter_by_incubationtemp
#NO UNIT TESTSfilter_by_staractivity
#NO UNIT TESTSfilter_by_cpgsensitivity
#NO UNIT TESTSfilter_by_damsensitivity
#NO UNIT TESTSfilter_by_dcmsensitivity
#NO UNIT TESTSfilter_by_bufferactivity
#NO UNIT TESTSfilter_by_vendor
#NO UNIT TESTSfilter_by_price
#NO UNIT TESTSfilter_by_sequence
#NO UNIT TESTSmutexclu
#NO UNIT TESTSCOPYRIGHT AND LICENSE
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