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Help: Option "use strand direction"

Here you can choose in which direction the entered sequences are interpreted. "5'-3'"-sequences are read from the 5' end to the 3' end from left to right. For the sequences in solution it is additionally possible to additionally let the program calculate the complementary sequence and use this as input. Writing the same sequence in both textboxes and choosing "use complementary sequence" will produce a perfect match.
The DNA-Chip producing company Affymetrix uses a syntax with identical sequences for probes and strands in the files documenting the sequences on their chips. (In the experiment cDNA (complementary DNA, i.e. DNA complementary to the mRNA from the cell lysate) is used. Therefore part of the mRNA will have the same sequence as the DNA on the chip.)

Example:
  Sequences on chip :

and
Sequences in solution :

will use the sequences 5'-GTCAACCA-3' and 5'-TGGTTGAC-3', which will be able to form the duplex:
5'-GTCAACCA-3'
3'-CAGTTGGT-5'

You will get the exact same result using this input:
  Sequences on chip :

and
Sequences in solution :

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Last modified: Tue Mar 28 18:56:16 CEST 2006