Cds |
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is
that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
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Chromosome |
Interval for the whole chromosome
If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
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ChromosomeSimpleName |
Convert chromosome names to simple names
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CircularCorrection |
Correct circular genomic coordinates
Nomenclature: We use coordinates at the beginning of the chromosme and negative coordinates
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Custom |
This is a custom interval (i.e.
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CytoBands |
Cytband definitions
E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
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Downstream |
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
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Exon |
Interval for an exon
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ExonSpliceCharacterizer |
Characterize exons based on alternative splicing
References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
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Gene |
Interval for a gene, as well as transcripts
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GenericMarker |
An interval intended as a mark
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Genes |
A collection of genes (marker intervals)
Note: It is assumed that all genes belong to the same genome
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Genome |
This is just used for the Interval class.
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GffMarker |
An interval intended as a mark
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Gtf2Marker |
An interval intended as a mark
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Intergenic |
Interval for in intergenic region
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IntergenicConserved |
Interval for a conserved intergenic region
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Interval |
A genomic interval.
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IntervalAndSubIntervals<T extends Marker> |
Interval that contains sub intervals.
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IntervalComparatorByEnd |
Compare intervals by end position
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IntervalComparatorByStart |
Compare intervals by start position
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IntervalSetIterator |
Iterate over intervals.
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Intron |
Intron
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IntronConserved |
Interval for a conserved non-coding region in an intron
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Marker |
An interval intended as a mark
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MarkerParentId |
This is a marker used as a 'fake' parent during data serialization
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Markers |
A collection of markers
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MarkerSeq |
Marker with a DNA sequence
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MarkerUtil |
Generic utility methods for Markers
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MicroRnaBindingSite |
miRna binding site (usually this was predicted by some algorithm)
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Motif |
Regulatory elements
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NextProt |
NextProt annotation marker
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ProteinInteractionLocus |
Protein interaction: An amino acid that is "in contact" with another amino acid.
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ProteinProteinInteractionLocus |
Protein interaction: An amino acid that is "in contact" with another amino acid
within the same protein.
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ProteinStructuralInteractionLocus |
Protein interaction: An amino acid that is "in contact" with another amino acid.
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RareAminoAcid |
Rare amino acid annotation:
These are amino acids that occurs very rarely in an organism.
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Regulation |
Regulatory elements
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SpliceSite |
Interval for a splice site
Reference: http://en.wikipedia.org/wiki/RNA_splicing
Spliceosomal introns often reside in eukaryotic protein-coding genes.
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SpliceSiteAcceptor |
Interval for a splice site acceptor
Note: Splice sites donnor are defined as the last 2 bases of an intron
Reference: http://en.wikipedia.org/wiki/RNA_splicing
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SpliceSiteBranch |
A (putative) branch site.
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SpliceSiteBranchU12 |
A (putative) U12 branch site.
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SpliceSiteDonor |
Interval for a splice site donnor
Note: Splice sites donnor are defined as the first 2 bases of an intron
Reference: http://en.wikipedia.org/wiki/RNA_splicing
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SpliceSiteRegion |
Interval for a splice site acceptor
From Sequence Ontology: A sequence variant in which a change has occurred
within the region of the splice site, either within 1-3 bases of the exon
or 3-8 bases of the intron.
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Transcript |
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
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Upstream |
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
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Utr |
Interval for a UTR (5 prime UTR and 3 prime UTR
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Utr3prime |
Interval for a UTR (5 prime UTR and 3 prime UTR
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Utr5prime |
Interval for a UTR (5 prime UTR and 3 prime UTR
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Variant |
A variant represents a change in a reference sequence
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VariantBnd |
A 'BND' variant (i.e.
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VariantNonRef |
A variant respect to non-reference (e.g.
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VariantWithScore |
A variant that has a numeric score.
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