# Package org.snpeff.interval

package org.snpeff.interval

Related Packages
Package
Description
org.snpeff
org.snpeff.interval.codonChange
org.snpeff.interval.tree
Class
Description
BioType
BioTypes: Gene or transcript bioType annotation References: http://www.ensembl.org/info/genome/genebuild/biotypes.html Biotypes classifies genes and transcripts into groups including: protein coding, pseudogene , processed pseudogene, miRNA, rRNA, scRNA, snoRNA, snRNA.
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.
Chromosome
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
ChromosomeSimpleName
Convert chromosome names to simple names
CircularCorrection
Correct circular genomic coordinates Nomenclature: We use coordinates at the beginning of the chromosme and negative coordinates
Custom
This is a custom interval (i.e.
CytoBands
Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
Downstream
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
Exon
Interval for an exon
Exon.ExonSpliceType
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
ExonSpliceCharacterizer
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
FrameType
Type of frame calculations Internally, we use GFF style frame calculation for Exon / Transcript Technically, these are 'frame' and 'phase' which are calculated in different ways UCSC type: Indicated the coding base number modulo 3.
Gene
Interval for a gene, as well as transcripts
Gene.GeneType
GenericMarker
An interval intended as a mark
Genes
A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genome
Genome
This is just used for the Interval class.
GffMarker
An interval intended as a mark
GffType
Gtf2Marker
An interval intended as a mark
Intergenic
Interval for in intergenic region
IntergenicConserved
Interval for a conserved intergenic region
Interval
A genomic interval.
IntervalAndSubIntervals<T extends Marker>
Interval that contains sub intervals.
IntervalComparatorByEnd
Compare intervals by end position
IntervalComparatorByStart
Compare intervals by start position
IntervalSetIterator
Iterate over intervals.
Intron
Intron
IntronConserved
Interval for a conserved non-coding region in an intron
Marker
An interval intended as a mark (i.e.
MarkerParentId
This is a marker used as a 'fake' parent during data serialization
Markers
A collection of markers
MarkerSeq
Marker with a DNA sequence
MarkerUtil
Generic utility methods for Markers
MarkerWithFrame
A Marker that has 'frame' information (Exon and Cds)
MicroRnaBindingSite
miRna binding site (usually this was predicted by some algorithm)
Motif
Regulatory elements
NextProt
NextProt annotation marker
ProteinInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.
ProteinProteinInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.
ProteinStructuralInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.
RareAminoAcid
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
Regulation
Regulatory elements
SpliceSite
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.
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
SpliceSiteBranch
A (putative) branch site.
SpliceSiteBranchU12
A (putative) U12 branch site.
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
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.
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
TranscriptSupportLevel
Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
Upstream
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
Utr
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr3prime
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr5prime
Interval for a UTR (5 prime UTR and 3 prime UTR
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
Variant.VariantType
VariantBnd
A 'BND' variant (i.e.
VariantNonRef
A variant respect to non-reference (e.g.
VariantWithScore
A variant that has a numeric score.