Extracting promoter sequence for reverse/minus strand gene from genome browser

Question

[amy.bashir]

Hello!

I would like to extract the promoter/upstream sequence of a gene from the genome of a non-model organism.

The gene is on the reverse strand, as can be seen below, with the region that I am interested in indicated by the red rectangle.

If I extract the sequence of this region on the genome browser, I should then convert the sequence to its reverse complement before doing any further analyses (like looking for motifs)?

Thank you very much for all your help!

[Joe]

It depends on your particular genome browsers default output. I would assume it will probably give you that span back for the top strand, so yes, you will need to reverse complement it before you do anything else.

[amy.bashir]

Great, thank you very much!

[WouterDeCoster]

How to add images to a Biostars post

Answer 1

[Alex Reynolds]

The answer can depend on what tool you use to search for motifs. For instance, FIMO will look for motifs on both strands unless you tell it not to, so in that case you would probably only need forward-stranded sequence.