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

Constants

Fragment

A Bio::RestrictionEnzyme::Fragment is a DNA fragment composed of fused primary and complementary strands that would be found floating in solution after a full sequence is digested by one or more RestrictionEnzymes.

You will notice that either the primary or complement strand will be padded with spaces to make them line up according to the original DNA configuration before they were cut.

Example:

Fragment 1:

primary =    "attaca"
complement = "  atga"

Fragment 2:

primary =    "g  "
complement = "cta"

View these with the primary and complement methods.

Bio::RestrictionEnzyme::Fragment is a simple Struct object.

Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragment

Public Class Methods

cut( sequence, enzymes ) click to toggle source

See Bio::RestrictionEnzyme::Analysis.cut

# File lib/bio/util/restriction_enzyme.rb, line 173
def self.cut( sequence, enzymes )
  Bio::RestrictionEnzyme::Analysis.cut( sequence, enzymes )
end
enzyme_name?( name ) click to toggle source

Check if supplied name is the name of an available enzyme

See Bio::REBASE#enzyme_name?


Arguments

  • name: Enzyme name

Returns

true or false

# File lib/bio/util/restriction_enzyme.rb, line 168
def self.enzyme_name?( name )
  self.rebase.enzyme_name?(name)
end
new(users_enzyme_or_rebase_or_pattern, *cut_locations) click to toggle source

See Bio::RestrictionEnzyme::DoubleStranded.new for more information.


Arguments

  • users_enzyme_or_rebase_or_pattern: One of three possible parameters: The name of an enzyme, a REBASE::EnzymeEntry object, or a nucleotide pattern with a cut mark.

  • cut_locations: The cut locations in enzyme index notation.

Returns

Bio::RestrictionEnzyme::DoubleStranded

# File lib/bio/util/restriction_enzyme.rb, line 142
def self.new(users_enzyme_or_rebase_or_pattern, *cut_locations)
  DoubleStranded.new(users_enzyme_or_rebase_or_pattern, *cut_locations)
end
rebase() click to toggle source

REBASE enzyme data information

Returns a Bio::REBASE object loaded with all of the enzyme data on file.


Arguments

  • none

Returns

Bio::REBASE

# File lib/bio/util/restriction_enzyme.rb, line 154
def self.rebase
  enzymes_yaml_file = File.join(File.dirname(File.expand_path(__FILE__)), 'restriction_enzyme', 'enzymes.yaml')
  @@rebase_enzymes ||= Bio::REBASE.load_yaml(enzymes_yaml_file)
  @@rebase_enzymes
end