Searching TATA box in the promoters of minus-strand genes
1
0
Entering edit mode
10.4 years ago
chjiao3456 ▴ 40

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~

TATA-box minus-strand • 3.6k views
ADD COMMENT
0
Entering edit mode
10.4 years ago

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

[AT]T[AT]TATA
____^
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1874 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6