Searching TATA box in the promoters of minus-strand genes

Question

[chjiao3456]

Hi, everyone, I'm trying to find whether the promoter region of one gene contain TATA box in the genome of C.elegans. I wrote a Perl script to search for motif "TATA[AT]A[AT]" from the DNA sequences generated by SAMTools from the genome fasta file. I'm confused that can I search TATA box in the promoter of genes on minus strand with the same motif? Or should I use the complementary motif "[AT]T[AT]TATA"? Thanks~

Answer 1

[Devon Ryan]

If it's on the opposite strand and not palindromic, then you need to take the reverse complement

[AT]T[AT]TATA
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[chjiao3456]

Thanks, I made a mistake in the reverse complementary motif.