Uses of Package
org.snpeff.interval
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Classes in org.snpeff.interval used by net.sf.samtools.tabix Class Description Variant A variant represents a change in a reference sequence Notes: This class was previously known as Variant. -
Classes in org.snpeff.interval used by org.snpeff Class Description Genome This is just used for the Interval class.Markers A collection of markersRegulation Regulatory elementsTranscriptSupportLevel 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 Notes: This class was previously known as Variant.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 markMarkerSeq 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 => InvalidGenome 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 -
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 => InvalidGenericMarker An interval intended as a markGenome This is just used for the Interval class.GffMarker An interval intended as a markMarker An interval intended as a markMarkers A collection of markersMotif Regulatory elementsRegulation Regulatory elementsVariant A variant represents a change in a reference sequence Notes: This class was previously known as Variant. -
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://vega.sanger.ac.uk/info/about/gene_and_transcript_types.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 => InvalidCustom This is a custom interval (i.e.CytoBands Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gzDownstream Interval for a gene, as well as some other information: exons, utrs, cds, etc.Exon Interval for an exonExon.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 transcriptsGene.GeneType GenericMarker An interval intended as a markGenes A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genomeGenome This is just used for the Interval class.GffMarker An interval intended as a markGffType Intergenic Interval for in intergenic regionInterval A genomic interval.IntervalAndSubIntervals Interval that contains sub intervals.Intron IntronMarker An interval intended as a markMarkers A collection of markersMarkerSeq Marker with a DNA sequenceMarkerWithFrame A Marker that has 'frame' information (Exon and Cds)MicroRnaBindingSite miRna binding site (usually this was predicted by some algorithm)Motif Regulatory elementsNextProt NextProt annotation markerProteinInteractionLocus 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 elementsSpliceSite 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_splicingSpliceSiteBranch 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_splicingSpliceSiteRegion 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=noUpstream 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 UTRUtr3prime Interval for a UTR (5 prime UTR and 3 prime UTRUtr5prime Interval for a UTR (5 prime UTR and 3 prime UTRVariant A variant represents a change in a reference sequence Notes: This class was previously known as Variant.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 exonMarker An interval intended as a markTranscript Interval for a transcript, as well as some other information: exons, utrs, cds, etc.Variant A variant represents a change in a reference sequence Notes: This class was previously known as Variant. -
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 markMarkers A collection of markers -
Classes in org.snpeff.interval used by org.snpeff.nextProt Class Description Markers A collection of markers -
Classes in org.snpeff.interval used by org.snpeff.outputFormatter Class Description Marker An interval intended as a mark -
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 -
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 markMarkers 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://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html Biotypes classifies genes and transcripts into groups including: protein coding, pseudogene , processed pseudogene, miRNA, rRNA, scRNA, snoRNA, snRNA.Exon Interval for an exonGene Interval for a gene, as well as transcriptsGenome This is just used for the Interval class.Intron IntronMarker An interval intended as a markMarkers A collection of markersTranscript 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=noVariant A variant represents a change in a reference sequence Notes: This class was previously known as Variant. -
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 => InvalidExon Interval for an exonGene Interval for a gene, as well as transcriptsGffMarker An interval intended as a markIntergenicConserved Interval for a conserved intergenic regionIntronConserved Interval for a conserved non-coding region in an intronMarker An interval intended as a markTranscript 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 UTRUtr5prime Interval for a UTR (5 prime UTR and 3 prime UTR -
Classes in org.snpeff.interval used by org.snpeff.snpEffect.testCases.integration Class Description Genome This is just used for the Interval class.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 Notes: This class was previously known as Variant. -
Classes in org.snpeff.interval used by org.snpeff.snpEffect.testCases.unity Class Description Chromosome Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => InvalidGene Interval for a gene, as well as transcriptsGenome This is just used for the Interval class.Marker An interval intended as a markMarkers A collection of markersTranscript Interval for a transcript, as well as some other information: exons, utrs, cds, etc.Variant A variant represents a change in a reference sequence Notes: This class was previously known as Variant.Variant.VariantType -
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 exonGene Interval for a gene, as well as transcriptsGenome This is just used for the Interval class.Marker An interval intended as a markMarkers A collection of markersTranscript Interval for a transcript, as well as some other information: exons, utrs, cds, etc.Variant A variant represents a change in a reference sequence Notes: This class was previously known as Variant.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 exonGene Interval for a gene, as well as transcriptsIntron IntronMarker An interval intended as a markMarkers A collection of markersTranscript 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://vega.sanger.ac.uk/info/about/gene_and_transcript_types.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 transcriptsInterval A genomic interval.Marker An interval intended as a markVariant A variant represents a change in a reference sequence Notes: This class was previously known as Variant.