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Prediction of gene class turned on by same stimulus
How to predict binding sites for key regulatory protein?
When the obvious is not enough
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You've already looked for possible NtcA-binding in the genome as judged by its consensus binding sequence, GTA..(8)..TAC, but the search gave you thousands of hits, and there certainly are not thousands of genes in the Anabaena genome regulated by NtcA!
The protein must sense something more than those six nucleotides when deciding where to bind. What can we do to go beyond the obvious as well? |
AATTTAGTATCAAAAATAACAATTCA
CGTTCTGTAACAAAGACTACAAAACT
AATTTTGTAGCTACTTATACTATTTT
AAAGCTGTAACAAAATCTACCAAATT
TCATTTGTACAGTCTGTTACCTTTAC
AAATCTGTAACATGAGATACACAATA
ATATCTGTAACATAAGCTACAAAATC
AAAATCGTAACAATTTATACGATTTT
ATTACTGTAACTAACTATACTAAATT
CGTTTGGTATCCAAGATAACTTTTTA
CCATCTGTAGGCTCTGTTACGTTTTC
GTA TAC
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