Uses of Package
org.snpeff.interval

Packages that use org.snpeff.interval
  • Classes in org.snpeff.interval used by org.snpeff
    Class
    Description
    This is just used for the Interval class.
    A collection of markers
    Regulatory elements
    Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
  • Class
    Description
    A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
     
  • Class
    Description
    This is just used for the Interval class.
    An interval intended as a mark (i.e.
    Marker with a DNA sequence
  • Class
    Description
    Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
    This is just used for the Interval class.
    Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
  • Class
    Description
    An interval intended as a mark (i.e.
  • Class
    Description
    Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
    An interval intended as a mark
    This is just used for the Interval class.
    An interval intended as a mark
    An interval intended as a mark (i.e.
    A collection of markers
    Regulatory elements
    Regulatory elements
    A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
  • Class
    Description
    This is just used for the Interval class.
    miRna binding site (usually this was predicted by some algorithm)
  • Class
    Description
    Interval for a gene, as well as transcripts
  • Class
    Description
    Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
  • Class
    Description
    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: 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 => Invalid
    This is a custom interval (i.e.
    Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
    Interval for a gene, as well as some other information: exons, utrs, cds, etc.
    Interval for an exon
    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 transcripts
     
    An interval intended as a mark
    A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genome
    This is just used for the Interval class.
    An interval intended as a mark
     
    Interval for in intergenic region
    A genomic interval.
    Interval that contains sub intervals.
    Intron
    An interval intended as a mark (i.e.
    A collection of markers
    Marker with a DNA sequence
    A Marker that has 'frame' information (Exon and Cds)
    miRna binding site (usually this was predicted by some algorithm)
    Regulatory elements
    NextProt annotation marker
    Protein 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 elements
    Interval 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_splicing
    A (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_splicing
    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.
    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=no
    Interval for a gene, as well as some other information: exons, utrs, cds, etc.
    Interval for a UTR (5 prime UTR and 3 prime UTR
    Interval for a UTR (5 prime UTR and 3 prime UTR
    Interval for a UTR (5 prime UTR and 3 prime UTR
    A 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.
  • Class
    Description
    Interval for an exon
    An 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.
  • Class
    Description
    This is just used for the Interval class.
    A genomic interval.
    An interval intended as a mark (i.e.
    A collection of markers
  • Class
    Description
    A collection of markers
    Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
  • Class
    Description
    An interval intended as a mark (i.e.
  • Class
    Description
    Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
  • Class
    Description
    This is just used for the Interval class.
    An interval intended as a mark (i.e.
  • Class
    Description
    This is just used for the Interval class.
    An interval intended as a mark (i.e.
    A collection of markers
  • Class
    Description
    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.
    Interval for an exon
    Interval for a gene, as well as transcripts
    This is just used for the Interval class.
    Intron
    An interval intended as a mark (i.e.
    A collection of markers
    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=no
    A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
  • Class
    Description
    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 => Invalid
    Interval for an exon
    Interval for a gene, as well as transcripts
    An interval intended as a mark
    Interval for a conserved intergenic region
    Interval for a conserved non-coding region in an intron
    An 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 UTR
    Interval for a UTR (5 prime UTR and 3 prime UTR
  • Class
    Description
    This 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.
  • Class
    Description
    Interval for an exon
    Interval for a gene, as well as transcripts
    This is just used for the Interval class.
    An interval intended as a mark (i.e.
    A collection of markers
    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.
     
    A 'BND' variant (i.e.
  • Class
    Description
    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 an exon
    Interval for a gene, as well as transcripts
    Intron
    An interval intended as a mark (i.e.
    A collection of markers
    Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
    A 'BND' variant (i.e.
  • Class
    Description
    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: 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 transcripts
    A 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.