class Bio::RestrictionEnzyme

Description ↑

Bio::RestrictionEnzyme allows you to fragment a DNA strand using one or more restriction enzymes. Bio::RestrictionEnzyme is aware that multiple enzymes may be competing for the same recognition site and returns the various possible fragmentation patterns that result in such circumstances.

When using Bio::RestrictionEnzyme you may simply use the name of common enzymes to cut your sequence or you may construct your own unique enzymes to use.

Visit the documentaion for individual classes for more information.

An examination of the unit tests will also reveal several interesting uses for the curious programmer.

Usage ↑

Basic ↑

EcoRI cut pattern:

G|A A T T C
 +-------+
C T T A A|G

This can also be written as:

G^AATTC

Note that to use the method cut_with_enzyme from a Bio::Sequence object you currently must require bio/util/restriction_enzyme directly. If instead you’re going to directly call Bio::RestrictionEnzyme::Analysis then only bio needs to be required.

require 'bio'
require 'bio/util/restriction_enzyme'

seq = Bio::Sequence::NA.new('gaattc')
cuts = seq.cut_with_enzyme('EcoRI')
cuts.primary                        # => ["aattc", "g"]
cuts.complement                     # => ["cttaa", "g"]
cuts.inspect                        # => "[#<struct Bio::RestrictionEnzyme::Fragment primary=\"g    \", complement=\"cttaa\">, #<struct Bio::RestrictionEnzyme::Fragment primary=\"aattc\", complement=\"    g\">]"

seq = Bio::Sequence::NA.new('gaattc')
cuts = seq.cut_with_enzyme('g^aattc')
cuts.primary                        # => ["aattc", "g"]
cuts.complement                     # => ["cttaa", "g"]

seq = Bio::Sequence::NA.new('gaattc')
cuts = seq.cut_with_enzyme('g^aattc', 'gaatt^c')
cuts.primary                        # => ["aattc", "c", "g", "gaatt"]
cuts.complement                     # => ["c", "cttaa", "g", "ttaag"]

seq = Bio::Sequence::NA.new('gaattcgaattc')
cuts = seq.cut_with_enzyme('EcoRI')
cuts.primary                        # => ["aattc", "aattcg", "g"]
cuts.complement                     # => ["cttaa", "g", "gcttaa"]

seq = Bio::Sequence::NA.new('gaattcgggaattc')
cuts = seq.cut_with_enzyme('EcoRI')
cuts.primary                        # => ["aattc", "aattcggg", "g"]
cuts.complement                     # => ["cttaa", "g", "gcccttaa"]

cuts[0].inspect                     # => "#<struct Bio::RestrictionEnzyme::Fragment primary=\"g    \", complement=\"cttaa\">"

cuts[0].primary                     # => "g    "
cuts[0].complement                  # => "cttaa"

cuts[1].primary                     # => "aattcggg    "
cuts[1].complement                  # => "    gcccttaa"

cuts[2].primary                     # => "aattc"
cuts[2].complement                  # => "    g"

Advanced ↑

require 'bio'

enzyme_1 = Bio::RestrictionEnzyme.new('anna', [1,1], [3,3])
enzyme_2 = Bio::RestrictionEnzyme.new('gg', [1,1])
a = Bio::RestrictionEnzyme::Analysis.cut('agga', enzyme_1, enzyme_2)
a.primary                           # => ["a", "ag", "g", "ga"]
a.complement                        # => ["c", "ct", "t", "tc"]

a[0].primary                        # => "ag"
a[0].complement                     # => "tc"

a[1].primary                        # => "ga"
a[1].complement                     # => "ct"

a[2].primary                        # => "a"
a[2].complement                     # => "t"

a[3].primary                        # => "g"
a[3].complement                     # => "c"

Todo / under development ↑