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 , , , C or , , , C.
  • The positions returned by GenomeLookup["seq"] are given in the form where is a chromosome specification, strand is or , and and are start and end positions.
  • Human chromosomes are specified as , , , 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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