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GenomeLookup

GenomeLookup["seq"]
returns the positions of exact matches for the DNA sequence seq on the reference human genome.
GenomeLookup["seq", n]
returns at most n matches.
  • 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.
EXAMPLESCLOSE ALL
Basic Examples   (3)
Find the positions of a DNA sequence fragment on the human genome:
Get the number of matches:
Get the first 10 matches:
Find the positions of a DNA sequence fragment on the human genome:
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Click for copyable input
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Get the number of matches:
In[1]:=
Click for copyable input
Out[1]=
 
Get the first 10 matches:
In[1]:=
Click for copyable input
Out[1]=
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