Uses of Package
org.snpeff.interval
Packages that use org.snpeff.interval
Package
Description
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Classes in org.snpeff.interval used by org.snpeffClassDescriptionThis is just used for the Interval class.A collection of markersRegulatory elementsTranscript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
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Classes in org.snpeff.interval used by org.snpeff.alignClassDescriptionA variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
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Classes in org.snpeff.interval used by org.snpeff.binseq
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Classes in org.snpeff.interval used by org.snpeff.codonsClassDescriptionInterval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => InvalidThis is just used for the Interval class.Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
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Classes in org.snpeff.interval used by org.snpeff.coverage
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Classes in org.snpeff.interval used by org.snpeff.fileIteratorClassDescriptionInterval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => InvalidAn interval intended as a markThis is just used for the Interval class.An interval intended as a markAn interval intended as a mark (i.e.A collection of markersRegulatory elementsRegulatory elementsA variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
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Classes in org.snpeff.interval used by org.snpeff.fileIterator.microCosmClassDescriptionThis is just used for the Interval class.miRna binding site (usually this was predicted by some algorithm)
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Classes in org.snpeff.interval used by org.snpeff.geneSets
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Classes in org.snpeff.interval used by org.snpeff.gsaClassDescriptionInterval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
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Classes in org.snpeff.interval used by org.snpeff.intervalClassDescriptionBioTypes: 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 => InvalidThis 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)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 markInterval for in intergenic regionA genomic interval.Interval that contains sub intervals.IntronAn interval intended as a mark (i.e.A collection of markersMarker with a DNA sequenceA 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.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.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 sequence As of version 4.0, variants have no strand, i.e.A variant that has a numeric score.
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Classes in org.snpeff.interval used by org.snpeff.interval.codonChangeClassDescriptionInterval for an exonAn interval intended as a mark (i.e.Interval for a transcript, as well as some other information: exons, utrs, cds, etc.A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
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Classes in org.snpeff.interval used by org.snpeff.interval.tree
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Classes in org.snpeff.interval used by org.snpeff.nextProtClassDescriptionA collection of markersInterval for a transcript, as well as some other information: exons, utrs, cds, etc.
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Classes in org.snpeff.interval used by org.snpeff.outputFormatter
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Classes in org.snpeff.interval used by org.snpeff.pdbClassDescriptionInterval for a transcript, as well as some other information: exons, utrs, cds, etc.
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Classes in org.snpeff.interval used by org.snpeff.probablility
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Classes in org.snpeff.interval used by org.snpeff.serializer
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Classes in org.snpeff.interval used by org.snpeff.snpEffectClassDescriptionBioTypes: 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.Interval for an exonInterval for a gene, as well as transcriptsThis is just used for the Interval class.IntronAn interval intended as a mark (i.e.A collection of markersInterval 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=noA variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
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Classes in org.snpeff.interval used by org.snpeff.snpEffect.factoryClassDescriptionCDS: 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 => InvalidInterval for an exonInterval for a gene, as well as transcriptsAn interval intended as a markInterval for a conserved intergenic regionInterval for a conserved non-coding region in an intronAn interval intended as a mark (i.e.Interval for a transcript, 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 UTR
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Classes in org.snpeff.interval used by org.snpeff.spliceSitesClassDescriptionThis is just used for the Interval class.A (putative) U12 branch site.Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
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Classes in org.snpeff.interval used by org.snpeff.statsClassDescriptionInterval for an exonInterval for a gene, as well as transcriptsThis is just used for the Interval class.An interval intended as a mark (i.e.A collection of markersInterval for a transcript, as well as some other information: exons, utrs, cds, etc.A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.A 'BND' variant (i.e.
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Classes in org.snpeff.interval used by org.snpeff.svgClassDescriptionCDS: 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 an exonInterval for a gene, as well as transcriptsIntronAn interval intended as a mark (i.e.A collection of markersInterval for a transcript, as well as some other information: exons, utrs, cds, etc.A 'BND' variant (i.e.
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Classes in org.snpeff.interval used by org.snpeff.vcfClassDescriptionBioTypes: 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 a gene, as well as transcriptsA genomic interval.An interval intended as a mark (i.e.A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.