GenomeData

GenomeData["gene"]
gives the DNA sequence for the specified gene on the reference human genome.

GenomeData["gene", "property"]
gives the value of the specified property for the human gene gene.

GenomeData[{"chr", {n1, n2}}]
gives the sequence from positions to on chromosome chr in the reference human genome.

DetailsDetails

  • Genes are specified by standard names such as .
  • GenomeData[] gives a list of human genes.
  • Human chromosomes can be specified as , , , etc., or by integers through , , , and .
  • GenomeData[{{"chr", +1}, {n1, n2}}] gives the 5' to 3' sequence from positions to on the top strand of chromosome chr. Sequence positions are measured relative to the 5' end of the top strand.
  • GenomeData[{{"chr", -1}, {m1, m2}}] gives the 5' to 3' sequence from positions to on the bottom strand of chromosome chr. Sequence positions are measured relative to the 5' end of the bottom strand.
  • Gene sequence properties include:
  • "FullSequence"the full sequence for the gene
    "FullSequencePosition"start and end positions of the gene
    "SequenceLength"length of the gene in base pairs
  • Gene location properties include:
  • "Chromosome"chromosome on which the gene is located
    "LocusList"locus for the gene as a list
    "LocusString"locus for the gene as a string
    "Orientation"forward (5' to 3') or reverse (3' to 5') as +1 or -1
  • Protein and transcription properties include:
  • "CodingSequenceLists"lists of coding sequences for the gene
    "CodingSequencePositions"lists of region positions for each coding sequence
    "CodingSequences"concatenated coding sequences for the gene
    "ExonSequences"list of sequences of exons for the gene
    "IntronSequences"list of sequences of introns for the gene
    "ProteinNames"names of the proteins coded for by the gene
    "UTRSequences"list of sequences of untranslated terminal regions of the gene
  • Functional properties include:
  • "BiologicalProcesses"biological processes associated with gene products
    "CellularComponents"cellular components in which gene products are found
    "InteractingGenes"genes interacting with this gene or its products
    "MolecularFunctions"molecular functions of gene products
  • Gene identification properties include:
  • "AlternateNames"common synonyms
    "GenBankIndices"GenBank index number strings
    "GeneID"GeneID number string
    "GeneOntologyIDs"Gene Ontology ID strings
    "MIMNumbers"Mendelian Inheritance in Man index number strings
    "Name"common English name
    "NCBIAccessions"NCBI accession strings
    "ProteinGenBankIndices"GenBank index number strings for protein products
    "ProteinNCBIAccessions"NCBI accession strings for protein products
    "StandardName"standard Mathematica name
    "TranscriptGenBankIndices"GenBank index number strings for RNA products
    "TranscriptNCBIAccessions"NCBI accession strings for RNA products
    "UniProtAccessions"UniProt accession strings
  • Overall properties of chromosomes include:
  • "SequenceLength"length of the chromosome in base pairs
    "UnsequencedPositions"start and end positions where the sequence is unknown
  • Properties related to lists of bands for chromosomes include:
  • "GBandLocusStrings"names of G-band loci
    "GBandScaledPositions"scaled start and end positions of all G-bands
    "GBandStainingCodes"cytogenetic staining codes for all G-bands
    "GBandStainingLevels"relative staining levels for all G-bands
  • GenomeData[gene, "prop", "ann"] gives various annotations associated with a property. Typical annotations include:
  • "Name"common English names
    "StandardName"standard Mathematica names
    "Units"units in which values are given

ExamplesExamplesopen allclose all

Basic Examples (5)Basic Examples (5)

Get the full DNA sequence of a gene on the human genome:

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Get the DNA sequence for part of a chromosome:

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Get a list of genes on a chromosome:

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Get the Mathematica standard name of the chromosome where a gene resides:

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Get the chromosome position of a gene:

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