# Uses of Package
org.snpeff.interval

Packages that use org.snpeff.interval
Package
Description
org.snpeff
org.snpeff.align
org.snpeff.binseq
org.snpeff.codons
org.snpeff.coverage
org.snpeff.fileIterator
org.snpeff.fileIterator.microCosm
org.snpeff.geneSets
org.snpeff.gsa
org.snpeff.interval
org.snpeff.interval.codonChange
org.snpeff.interval.tree
org.snpeff.nextProt
org.snpeff.outputFormatter
org.snpeff.pdb
org.snpeff.probablility
org.snpeff.serializer
org.snpeff.snpEffect
org.snpeff.snpEffect.factory
org.snpeff.spliceSites
org.snpeff.stats
org.snpeff.svg
org.snpeff.vcf

Classes in org.snpeff.interval used by org.snpeff
Class
Description
Genome
This is just used for the Interval class.
Markers
A collection of markers
Regulation
Regulatory elements
TranscriptSupportLevel
Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
Classes in org.snpeff.interval used by org.snpeff.align
Class
Description
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
Variant.VariantType
Classes in org.snpeff.interval used by org.snpeff.binseq
Class
Description
Genome
This is just used for the Interval class.
Marker
An interval intended as a mark (i.e.
MarkerSeq
Marker with a DNA sequence
Classes in org.snpeff.interval used by org.snpeff.codons
Class
Description
Chromosome
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
Genome
This is just used for the Interval class.
RareAminoAcid
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
Classes in org.snpeff.interval used by org.snpeff.coverage
Class
Description
Marker
An interval intended as a mark (i.e.
Classes in org.snpeff.interval used by org.snpeff.fileIterator
Class
Description
Chromosome
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
GenericMarker
An interval intended as a mark
Genome
This is just used for the Interval class.
GffMarker
An interval intended as a mark
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
Motif
Regulatory elements
Regulation
Regulatory elements
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
Classes in org.snpeff.interval used by org.snpeff.fileIterator.microCosm
Class
Description
Genome
This is just used for the Interval class.
MicroRnaBindingSite
miRna binding site (usually this was predicted by some algorithm)
Classes in org.snpeff.interval used by org.snpeff.geneSets
Class
Description
Gene
Interval for a gene, as well as transcripts
Classes in org.snpeff.interval used by org.snpeff.gsa
Class
Description
Chromosome
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
Classes in org.snpeff.interval used by org.snpeff.interval
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
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)
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
Intergenic
Interval for in intergenic region
Interval
A genomic interval.
IntervalAndSubIntervals
Interval that contains sub intervals.
Intron
Intron
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
MarkerSeq
Marker with a DNA sequence
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.
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.
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
VariantWithScore
A variant that has a numeric score.
Classes in org.snpeff.interval used by org.snpeff.interval.codonChange
Class
Description
Exon
Interval for an exon
Marker
An interval intended as a mark (i.e.
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
Classes in org.snpeff.interval used by org.snpeff.interval.tree
Class
Description
Genome
This is just used for the Interval class.
Interval
A genomic interval.
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
Classes in org.snpeff.interval used by org.snpeff.nextProt
Class
Description
Markers
A collection of markers
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
Classes in org.snpeff.interval used by org.snpeff.outputFormatter
Class
Description
Marker
An interval intended as a mark (i.e.
Classes in org.snpeff.interval used by org.snpeff.pdb
Class
Description
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
Classes in org.snpeff.interval used by org.snpeff.probablility
Class
Description
Genome
This is just used for the Interval class.
Marker
An interval intended as a mark (i.e.
Classes in org.snpeff.interval used by org.snpeff.serializer
Class
Description
Genome
This is just used for the Interval class.
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
Classes in org.snpeff.interval used by org.snpeff.snpEffect
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.
Exon
Interval for an exon
Gene
Interval for a gene, as well as transcripts
Genome
This is just used for the Interval class.
Intron
Intron
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
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
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
Classes in org.snpeff.interval used by org.snpeff.snpEffect.factory
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
Exon
Interval for an exon
Gene
Interval for a gene, as well as transcripts
GffMarker
An interval intended as a mark
IntergenicConserved
Interval for a conserved intergenic region
IntronConserved
Interval for a conserved non-coding region in an intron
Marker
An interval intended as a mark (i.e.
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
Utr3prime
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr5prime
Interval for a UTR (5 prime UTR and 3 prime UTR
Classes in org.snpeff.interval used by org.snpeff.spliceSites
Class
Description
Genome
This is just used for the Interval class.
SpliceSiteBranchU12
A (putative) U12 branch site.
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
Classes in org.snpeff.interval used by org.snpeff.stats
Class
Description
Exon
Interval for an exon
Gene
Interval for a gene, as well as transcripts
Genome
This is just used for the Interval class.
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
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.
Classes in org.snpeff.interval used by org.snpeff.svg
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.
Exon
Interval for an exon
Gene
Interval for a gene, as well as transcripts
Intron
Intron
Marker
An interval intended as a mark (i.e.
Markers
A collection of markers
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
VariantBnd
A 'BND' variant (i.e.
Classes in org.snpeff.interval used by org.snpeff.vcf
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.
Gene
Interval for a gene, as well as transcripts
Interval
A genomic interval.
Marker
An interval intended as a mark (i.e.
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.