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GenomeLookup
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GenomeLookup

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GenomeLookup["seq"]

returns the positions of exact matches for the DNA sequence seq on the reference human genome.

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GenomeLookup["seq",n]

returns at most n matches.

Details

  • Sequences are represented as strings containing A, T, G, C or A, U, G, C.
  • The positions returned by GenomeLookup["seq"] are given in the form {{"chr",strand},{p1,p2}} where "chr" is a chromosome specification, strand is +1 or -1, and p1 and p2 are start and end positions.
  • Human chromosomes are specified as "Chromosome1", "ChromosomeX", "Mitochondrion", etc.
  • Bases are numbered in the 5' to 3' direction of the specified strand.
  • GenomeLookup[spec,"Count"] gives a count of the number of exact matches.

Examples

Basic Examples  (3)Summary of the most common use cases

Find the positions of a DNA sequence fragment on the human genome:

In[1]:=1
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https://wolfram.com/xid/0v50kne0nula0-jjfhgc
Out[1]=1

Get the number of matches:

In[1]:=1
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https://wolfram.com/xid/0v50kne0nula0-ivkrpl
Out[1]=1

Get the first 10 matches:

In[1]:=1
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https://wolfram.com/xid/0v50kne0nula0-ymmeyz
Out[1]=1
Wolfram Research (2008), GenomeLookup, Wolfram Language function, https://reference.wolfram.com/language/ref/GenomeLookup.html.
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Wolfram Research (2008), GenomeLookup, Wolfram Language function, https://reference.wolfram.com/language/ref/GenomeLookup.html.

Text

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

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

CMS

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

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

APA

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

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

BibTeX

@misc{reference.wolfram_2025_genomelookup, author="Wolfram Research", title="{GenomeLookup}", year="2008", howpublished="\url{https://reference.wolfram.com/language/ref/GenomeLookup.html}", note=[Accessed: 04-May-2025 ]}

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@misc{reference.wolfram_2025_genomelookup, author="Wolfram Research", title="{GenomeLookup}", year="2008", howpublished="\url{https://reference.wolfram.com/language/ref/GenomeLookup.html}", note=[Accessed: 04-May-2025 ]}

BibLaTeX

@online{reference.wolfram_2025_genomelookup, organization={Wolfram Research}, title={GenomeLookup}, year={2008}, url={https://reference.wolfram.com/language/ref/GenomeLookup.html}, note=[Accessed: 04-May-2025 ]}

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@online{reference.wolfram_2025_genomelookup, organization={Wolfram Research}, title={GenomeLookup}, year={2008}, url={https://reference.wolfram.com/language/ref/GenomeLookup.html}, note=[Accessed: 04-May-2025 ]}