BUILT-IN MATHEMATICA SYMBOL
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.
- 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 |
Get the full DNA sequence of a gene on the human genome:
Out[1]//Short= |
| |  |
| Out[2]= |  |
Get the DNA sequence for part of a chromosome:
| Out[1]= |  |
Get a list of genes on a chromosome:
Out[1]//Short= |
| |  |
Get the Mathematica standard name of the chromosome where a gene resides:
| Out[1]= |  |
Get the chromosome position of a gene:
| Out[1]= |  |
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