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.

DetailsDetails

  • 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.

ExamplesExamplesopen allclose all

Basic Examples  (3)Basic Examples  (3)

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

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Get the number of matches:

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Get the first 10 matches:

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Introduced in 2008
(7.0)