CodingSequence Class |
Namespace: Bio.IO.GenBank
The CodingSequence type exposes the following members.
Name | Description | |
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CodingSequence(String) |
Creates new CodingSequence feature item with the specified location.
Note that this constructor uses LocationBuilder to construct location object from the specified
location string.
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CodingSequence(ILocation) |
Creates new CodingSequence feature item from the specified location.
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Name | Description | |
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Allele |
Name of the allele for the given gene.
All gene-related features (exon, CDS etc) for a given gene should share the same Allele qualifier value;
the Allele qualifier value must, by definition, be different from the Gene qualifier value; when used with
the variation feature key, the Allele qualifier value should be that of the variant.
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Citation |
Reference to a citation listed in the entry reference field.
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Codon |
Specifies a codon which is different from any found in the reference genetic code.
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CodonStart |
Indicates the offset at which the first complete codon of a coding feature can be found,
relative to the first base of that feature.
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DatabaseCrossReference |
Database cross-reference: pointer to related information in another database.
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EnzymeCommissionNumber |
Enzyme Commission number for enzyme product of sequence.
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Exception |
Indicates that the coding region cannot be translated using standard biological rules.
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Experiment |
A brief description of the nature of the experimental evidence that supports the feature
identification or assignment.
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Function |
Function attributed to a sequence.
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GeneSymbol |
Symbol of the gene corresponding to a sequence region.
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GeneSynonym |
Synonymous, replaced, obsolete or former gene symbol.
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GenomicMapPosition |
Genomic map position of feature.
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Inference |
A structured description of non-experimental evidence that supports the feature
identification or assignment.
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Key |
Gets the key for this item. These are not necessarily unique within a list,
which is why this is a property of an object to be included in a list, rather than
omitting this as a property and using a dictionary instead of a list.
(Inherited from FeatureItem.) | |
Label |
A label used to permanently tag a feature.
(Inherited from FeatureItem.) | |
Location |
Gets the location of this feature in the sequence.
This may also refers to other genbank files.
For example,
join(100..200,J00194.1:1..150)
In this example location specifies joining of bases from 100 to 200 from the sequence
in which this location data present and bases from 1 to 150 from the sequence who's
accession number is J00194.1.
(Inherited from FeatureItem.) | |
LocusTag |
A submitter-supplied, systematic, stable identifier for a gene and its associated
features, used for tracking purposes.
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Note |
Any comment or additional information.
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Number |
A number to indicate the order of genetic elements (e.g., exons or introns) in the 5' to 3' direction.
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OldLocusTag |
Feature tag assigned for tracking purposes.
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Operon |
Name of the group of contiguous genes transcribed into a single transcript to which that feature belongs.
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Product |
Name of the product associated with the feature, e.g. the mRNA of an mRNA feature,
the polypeptide of a CDS, the mature peptide of a mat_peptide, etc.
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ProteinId |
Protein identifier, issued by International collaborators. this qualifier consists of a stable ID
portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point.
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Pseudo |
Indicates that this feature is a non-functional version of the element named by the feature key.
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Qualifiers |
Gets the dictionary of attributes.
(Inherited from FeatureItem.) | |
RibosomalSlippage |
During protein translation, certain sequences can program ribosomes to change to an alternative
reading frame by a mechanism known as ribosomal slippage.
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StandardName |
Accepted standard name for this feature.
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Translation |
Automatically generated one-letter abbreviated amino acid sequence derived from either
the universal genetic code or the table as specified in Transl_table qualifier and as
determined by exceptions in the Transl_except and Codon qualifiers.
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TranslationalExcept |
Translational exception: single codon the translation of which does not conform
to genetic code defined by Organism and Codon qualifier.
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TranslationTable |
Definition of genetic code table used if other than universal genetic code table.
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TransSplicing |
Indicates that exons from two RNA molecules are ligated in intermolecular
reaction to form mature RNA.
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Name | Description | |
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Clone |
Creates a new CodingSequence that is a copy of the current CodingSequence.
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Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) | |
Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) | |
GetHashCode | Serves as the default hash function. (Inherited from Object.) | |
GetQualifier |
Returns list of qualifier values for the specified qualifier name.
(Inherited from FeatureItem.) | |
GetSingleBooleanQualifier |
Returns bool value indicating whether the specified qualifier is there in the feature or not.
(Inherited from FeatureItem.) | |
GetSingleTextQualifier |
Returns qualifier value for the specified qualifier name.
Note: This method should be used to get the text value of a
qualifier which appears only once in a feature.
(Inherited from FeatureItem.) | |
GetSubFeatures |
Gets the sub features depending on the location information.
(Inherited from FeatureItem.) | |
GetSubSequence(ISequence) |
Returns a new sequence from the specified sequence which contains bases of this feature as specified by
the location property of this feature.
(Inherited from FeatureItem.) | |
GetSubSequence(ISequence, DictionaryString, ISequence) |
Returns a sequence which contains bases from the specified sequences as specified by this feature location.
If the location contains accession then the sequence from the referredSequences which matches the
accession of the location will be considered.
For example,
If a location is "join(100..200, J00089.1:10..50, J00090.2:30..40)"
bases from 100 to 200 will be taken from the parent sequence and referredSequences will
be searched for the J00089.1 and J00090.2 accession if found then those sequences will be considered
for constructing the output sequence.
If the referred sequence is not found in the referredSequences then an exception will occur.
(Inherited from FeatureItem.) | |
GetTranslation |
Returns protein sequence from the translation.
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GetType | Gets the Type of the current instance. (Inherited from Object.) | |
MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) | |
SetSingleBooleanQualifier |
Sets the value for the specified qualifier name.
Note: This method should be used to add a qualifier which
appears only once in a feature and whose value is none.
(Inherited from FeatureItem.) | |
SetSingleTextQualifier |
Sets the value for the specified qualifier name.
Note: This method should be used to set the text value of a
qualifier which appears only once in a feature.
(Inherited from FeatureItem.) | |
ToString | Returns a string that represents the current object. (Inherited from Object.) |