Package org.snpeff.interval
package org.snpeff.interval
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ClassDescriptionBioTypes: 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: 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.Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => InvalidConvert chromosome names to simple namesCorrect circular genomic coordinates Nomenclature: We use coordinates at the beginning of the chromosme and negative coordinatesThis is a custom interval (i.e.Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gzInterval for a gene, as well as some other information: exons, utrs, cds, etc.Interval for an exonCharacterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)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.Interval for a gene, as well as transcriptsAn interval intended as a markA collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genomeThis is just used for the Interval class.An interval intended as a markAn interval intended as a markInterval for in intergenic regionInterval for a conserved intergenic regionA genomic interval.IntervalAndSubIntervals<T extends Marker>Interval that contains sub intervals.Compare intervals by end positionCompare intervals by start positionIterate over intervals.IntronInterval for a conserved non-coding region in an intronAn interval intended as a markThis is a marker used as a 'fake' parent during data serializationA collection of markersMarker with a DNA sequenceGeneric utility methods for MarkersA Marker that has 'frame' information (Exon and Cds)miRna binding site (usually this was predicted by some algorithm)Regulatory elementsNextProt annotation markerProtein interaction: An amino acid that is "in contact" with another amino acid.Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.Protein interaction: An amino acid that is "in contact" with another amino acid.Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.Regulatory elementsInterval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.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_splicingA (putative) branch site.A (putative) U12 branch site.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_splicingInterval 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.Interval for a transcript, as well as some other information: exons, utrs, cds, etc.Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=noInterval for a gene, as well as some other information: exons, utrs, cds, etc.Interval for a UTR (5 prime UTR and 3 prime UTRInterval for a UTR (5 prime UTR and 3 prime UTRInterval for a UTR (5 prime UTR and 3 prime UTRA variant represents a change in a reference sequenceA 'BND' variant (i.e.A variant respect to non-reference (e.g.A variant that has a numeric score.