Question: Extracting promoter sequence for reverse/minus strand gene from genome browser
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gravatar for amy.bashir
6 months ago by
amy.bashir80
amy.bashir80 wrote:

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.

image

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!

ADD COMMENTlink modified 4 months ago by Alex Reynolds26k • written 6 months ago by amy.bashir80
2

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.

ADD REPLYlink written 6 months ago by jrj.healey9.1k

Great, thank you very much!

ADD REPLYlink written 6 months ago by amy.bashir80

How to add images to a Biostars post

ADD REPLYlink written 6 months ago by WouterDeCoster35k
0
gravatar for Alex Reynolds
4 months ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

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.

ADD COMMENTlink written 4 months ago by Alex Reynolds26k
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