Question: How to identify strand of a gene in bacteria?
0
gravatar for Pranavathiyani G
2.2 years ago by
Pondicherry, India
Pranavathiyani G310 wrote:

I have a list of genes (sequences) from bacteria and also have the whole genome sequence, how can i know the genes are encoded in positive strand or negative strand? Is there any possible way to find out?

ADD COMMENTlink modified 24 months ago by Biostar ♦♦ 20 • written 2.2 years ago by Pranavathiyani G310

If the annotations are available, you can search for strand information.

ADD REPLYlink written 2.2 years ago by cpad011213k

If it's not available, is there any way to find it?

ADD REPLYlink written 2.2 years ago by Pranavathiyani G310

Perform a re-alignment to the genome using your sequences. Just use something simple like HISAT2 followed by StringTie, and then you can infer the strand to which the reads have aligned. I have done this before with bacteria and it works quite well.

ADD REPLYlink written 2.2 years ago by Kevin Blighe61k

Align (blast) gene sequences to reference sequence. If gene sequences align to reference sequence, then it is the on the same direction of your reference. If it aligns to complementary strand of reference sequence, then it is on the other strand.

ADD REPLYlink written 2.2 years ago by cpad011213k

Yeah a simple blast can do it.

ADD REPLYlink written 24 months ago by Dattatray Mongad350
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