Class RestrictionEnzymeManager
RestrictionEnzymeManager
manages collections of
static RestrictionEnzyme
instances. A properties file
should be placed in the CLASSPATH containing a key
"rebase.data.file" and a corresponding value of a REBASE file
(standard REBASE format #31 conventionally named withrefm.### where
### is the version number). This file will be loaded by the
RestrictionEnzymeManager
ClassLoader
. The
properties are loaded as a ResourceBundle
, so the file
should be named "RestrictionEnzymeManager.properties".
Since 1.5, a format #31 REBASE file can be loaded at anytime
using the method loadEnzymeFile
and optionally filtered
for commercially available enzymes.
- Since:
- 1.3
- Author:
- Keith James, George Waldon
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
REBASE_DATA_KEY
the ResourceBundle key which specifies the location of the REBASE flat file.static final String
REBASE_TAG_COMM
the REBASE tag containing the commercial suppliers.static final String
REBASE_TAG_ISZR
the REBASE tag containing the enzyme isoschizomers.static final String
REBASE_TAG_METH
the REBASE tag containing the methylation site.static final String
REBASE_TAG_NAME
the REBASE tag containing the enzyme name.static final String
REBASE_TAG_ORGN
the REBASE tag containing the organism.static final String
REBASE_TAG_REFS
the REBASE tag containing the references.static final String
REBASE_TAG_SITE
the REBASE tag containing the enzyme site.static final String
REBASE_TAG_SRCE
the REBASE tag containing the source. -
Method Summary
Modifier and TypeMethodDescriptionstatic Set
getAllEnzymes
returns an unmodifable set of all available enzymes.static Annotation
getAnnotation
(RestrictionEnzyme enzyme) getAnnotation
returns an immutable, static annotation describing the enzyme.static RestrictionEnzyme
getEnzyme
returns an enzyme by name.static Set
getIsoschizomers
(String name) getIsoschizomers
returns an unmodifable set of the isoschizomers of this enzyme.static Set
getNCutters
(int n) getNCutters
returns an unmodifable set of all enzymes with a cut site of size n.static Pattern[]
getPatterns
(RestrictionEnzyme enzyme) getPatterns
returns twoPattern
objects for an enzyme, one matches the forward strand and one the reverse.static String
getRecognitionSequence
(String name) getRecognitionSequence
returns a string that describes the recognition site of this enzyme.static String
getSuppliers
(RestrictionEnzyme enzyme) getSuppliers
returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.static void
loadEnzymeFile
(InputStream is, boolean commercialOnly) loadEnzymeFile
loads a new REBASE file (or any file using REBASE format #31).static void
register
(RestrictionEnzyme enzyme, Set isoschizomers) register
regisiters a newRestrictionEnzyme
with the manager.
-
Field Details
-
REBASE_DATA_KEY
REBASE_DATA_KEY
the ResourceBundle key which specifies the location of the REBASE flat file.- See Also:
-
REBASE_TAG_NAME
REBASE_TAG_NAME
the REBASE tag containing the enzyme name.- See Also:
-
REBASE_TAG_ISZR
REBASE_TAG_ISZR
the REBASE tag containing the enzyme isoschizomers.- See Also:
-
REBASE_TAG_SITE
REBASE_TAG_SITE
the REBASE tag containing the enzyme site.- See Also:
-
REBASE_TAG_METH
REBASE_TAG_METH
the REBASE tag containing the methylation site.- See Also:
-
REBASE_TAG_ORGN
REBASE_TAG_ORGN
the REBASE tag containing the organism.- See Also:
-
REBASE_TAG_SRCE
REBASE_TAG_SRCE
the REBASE tag containing the source.- See Also:
-
REBASE_TAG_COMM
REBASE_TAG_COMM
the REBASE tag containing the commercial suppliers.- See Also:
-
REBASE_TAG_REFS
REBASE_TAG_REFS
the REBASE tag containing the references.- See Also:
-
-
Method Details
-
loadEnzymeFile
loadEnzymeFile
loads a new REBASE file (or any file using REBASE format #31).- Parameters:
is
- an InputStream over the file to load.commercialOnly
- indicates whether or not only commercially available enzymes are loaded.- Since:
- 1.5
-
getAllEnzymes
getAllEnzymes
returns an unmodifable set of all available enzymes.- Returns:
- a
Set
ofRestrictionEnzyme
s.
-
getEnzyme
getEnzyme
returns an enzyme by name.- Parameters:
name
- aString
such as EcoRI, case sensitive.- Returns:
- a
RestrictionEnzyme
.
-
getIsoschizomers
getIsoschizomers
returns an unmodifable set of the isoschizomers of this enzyme.- Parameters:
name
- aString
such as EcoRI, case sensitive.- Returns:
- a
Set
ofRestrictionEnzyme
s.
-
getRecognitionSequence
getRecognitionSequence
returns a string that describes the recognition site of this enzyme. It corresponds to the field invalid input: '<'3> of the REBASE file.- Parameters:
name
- aString
such as EcoRI, case sensitive.- Returns:
- a
String
describing the recognition sequence, e.g. "G^AATTC" for EcoRI. - Since:
- 1.5
-
getNCutters
getNCutters
returns an unmodifable set of all enzymes with a cut site of size n.- Parameters:
n
- anint
cut site size.- Returns:
- a
Set
ofRestrictionEnzyme
s.
-
getPatterns
getPatterns
returns twoPattern
objects for an enzyme, one matches the forward strand and one the reverse. This enables searching of both strands of a sequence without reverse-complementing it. AsPattern
objects are thread-safe these may be used for all searches.- Parameters:
enzyme
- aRestrictionEnzyme
.- Returns:
- a
Pattern []
array with the forward strandPattern
at index 0 and the reverse at index 1.
-
getAnnotation
getAnnotation
returns an immutable, static annotation describing the enzyme. This is suitable for adding toFeature
s which represent restriction sites. The annotation produced currently contains one key "dbxref" in line with the GenBank/EMBL qualifier for the "misc_binding" feature key. The key has a corresponding value "REBASE:<enzyme name>".- Parameters:
enzyme
- aRestrictionEnzyme
.- Returns:
- an
Annotation
.
-
getSuppliers
getSuppliers
returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.REBASE #31 version 604 code:
A GE Healthcare (8/05)
B Invitrogen Corporation(8/05)
C Minotech Biotechnology (9/05)
E Stratagene (9/05)
F Fermentas International Inc. (2/06)
G Qbiogene (9/05)
H American Allied Biochemical, Inc. (9/05)
I SibEnzyme Ltd. (2/06)
J Nippon Gene Co., Ltd. (8/05)
K Takara Bio Inc. (9/05)
M Roche Applied Science (8/05)
N New England Biolabs (2/06)
O Toyobo Biochemicals (9/05)
Q Molecular Biology Resources (8/05)
R Promega Corporation (9/05)
S Sigma Chemical Corporation (9/05)
U Bangalore Genei (9/05)
V Vivantis Technologies (1/06)
X EURx Ltd. (9/05)
Y CinnaGen Inc. (9/05)- Parameters:
enzyme
- aRestrictionEnzyme
.- Returns:
- a
String
. - Since:
- 1.5
-
register
register
regisiters a newRestrictionEnzyme
with the manager. It does not check that the isoschizomers are known to the manager. If there are custom isoschizomers in theSet
, they should be also be registered.- Parameters:
enzyme
- aRestrictionEnzyme
to register.isoschizomers
- aSet
ofRestrictionEnzyme
s which are isoschizomers.
-