Package org.snpeff.interval

Interface Summary

Interface	Description
MarkerWithFrame	A Marker that has 'frame' information (Exon and Cds)

Class Summary

Class	Description
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
ExonSpliceCharacterizer	Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
Gene	Interval for a gene, as well as transcripts
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
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
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
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.
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
VariantBnd	A 'BND' variant (i.e.
VariantNonRef	A variant respect to non-reference (e.g.
VariantWithScore	A variant that has a numeric score.

Enum Summary

Enum	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.
Exon.ExonSpliceType	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.GeneType
GffType
TranscriptSupportLevel	Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
Variant.VariantType