WOLFRAM

Wolfram Language & System Documentation Center
Wolfram Language Home Page »

GenomeData
✖
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 n1 to n2 on chromosome chr in the reference human genome.

Details

  • Genes are specified by standard names such as "BRCA1".
  • GenomeData[] gives a list of human genes.
  • Human chromosomes can be specified as "Chromosome1", "ChromosomeX", "Mitochondrion", etc., or by integers 1 through 22, "X", "Y", and "MT".
  • GenomeData[{{"chr",+1},{n1,n2}}] gives the 5' to 3' sequence from positions n1 to n2 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 m1 to m2 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
    "UnitsStandardName"standard Wolfram Language 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
    "UnitsStandardName"standard Wolfram Language names
    "Units"units in which values are given

Examples

open allclose all

Basic Examples  (5)Summary of the most common use cases

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

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-yarnni
In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-lz3ql
Out[2]=2

Get the DNA sequence for part of a chromosome:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-qemle8
Out[1]=1

Get a list of genes on a chromosome:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-gv1hvr

Get the Wolfram Language standard name of the chromosome where a gene resides:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-071mut
Out[1]=1

Get the chromosome position of a gene:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-3lvuvv
Out[1]=1

Scope  (9)Survey of the scope of standard use cases

Names and Classes  (5)

Obtain a list of gene names:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-z62ey8

Find the English name of a gene:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-kg5e0v
Out[1]=1

Get a list of gene classes:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-jxj3qm

Get a list of genes involved in signal transduction:

In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-l8d4bp

Get a list of classes a gene belongs to:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-k5xdkh
Out[1]=1

Test whether a gene belongs to a class:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-vnd66u
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-b62lpn
Out[2]=2

Gene and Chromosome Sequences  (4)

Get the DNA sequence of a gene:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-sdjhd
In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-g0om0n
Out[2]=2

Get the chromosome position of a gene:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-k89yvn
Out[1]=1

Get the Wolfram Language standard name of the chromosome where a gene resides:

In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-zm9pko
Out[2]=2

Get the orientation of the gene on the chromosome:

In[3]:=3
✖
https://wolfram.com/xid/0h2ol8ixq6-g8b1ae
Out[3]=3

Get the DNA sequence for part of a chromosome on the bottom strand:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-0d49tc
Out[1]=1

Get the positions of coding sequences for a gene:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-ya3zlg
Out[1]=1

Applications  (4)Sample problems that can be solved with this function

Make a log plot of the distribution of lengths of human chromosomes:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-b8f60g
Out[1]=1

Make a log rank plot of the lengths of genes for human chromosome 22:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-l1ddx
Out[1]=1

Make a plot of average coding sequence length versus gene length:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-03qbzh
Out[1]=1

Visualize a gene as an image:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-p3v0k
In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-n4wv1h
Out[2]=2

Show the first 20 genes on chromosome 12:

In[3]:=3
✖
https://wolfram.com/xid/0h2ol8ixq6-btf087
Out[3]=3

Properties & Relations  (2)Properties of the function, and connections to other functions

Get a sequence from the top strand of chromosome 1:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-3o4j0b
Out[1]=1

Get the complementary sequence from the bottom strand:

In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-dv70iz
Out[2]=2

Show that the bottom strand is complementary to the top strand:

In[3]:=3
✖
https://wolfram.com/xid/0h2ol8ixq6-wnzk2o
Out[3]=3

Use GenomeData to extract the sequences found by GenomeLookup:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-t7ss6c
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0h2ol8ixq6-w41dl9
Out[2]=2

Neat Examples  (1)Surprising or curious use cases

Find the 5 shortest genes in the human genome:

In[1]:=1
✖
https://wolfram.com/xid/0h2ol8ixq6-cj116t
Out[1]=1
Wolfram Research (2008), GenomeData, Wolfram Language function, https://reference.wolfram.com/language/ref/GenomeData.html.
✖
Wolfram Research (2008), GenomeData, Wolfram Language function, https://reference.wolfram.com/language/ref/GenomeData.html.

Text

Wolfram Research (2008), GenomeData, Wolfram Language function, https://reference.wolfram.com/language/ref/GenomeData.html.

✖
Wolfram Research (2008), GenomeData, Wolfram Language function, https://reference.wolfram.com/language/ref/GenomeData.html.

CMS

Wolfram Language. 2008. "GenomeData." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/GenomeData.html.

✖
Wolfram Language. 2008. "GenomeData." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/GenomeData.html.

APA

Wolfram Language. (2008). GenomeData. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/GenomeData.html

✖
Wolfram Language. (2008). GenomeData. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/GenomeData.html

BibTeX

@misc{reference.wolfram_2025_genomedata, author="Wolfram Research", title="{GenomeData}", year="2008", howpublished="\url{https://reference.wolfram.com/language/ref/GenomeData.html}", note=[Accessed: 25-March-2025 ]}

✖
@misc{reference.wolfram_2025_genomedata, author="Wolfram Research", title="{GenomeData}", year="2008", howpublished="\url{https://reference.wolfram.com/language/ref/GenomeData.html}", note=[Accessed: 25-March-2025 ]}

BibLaTeX

@online{reference.wolfram_2025_genomedata, organization={Wolfram Research}, title={GenomeData}, year={2008}, url={https://reference.wolfram.com/language/ref/GenomeData.html}, note=[Accessed: 25-March-2025 ]}

✖
@online{reference.wolfram_2025_genomedata, organization={Wolfram Research}, title={GenomeData}, year={2008}, url={https://reference.wolfram.com/language/ref/GenomeData.html}, note=[Accessed: 25-March-2025 ]}