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How to identify strand of a gene in bacteria?
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17 months ago
Pondicherry, India

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?

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

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

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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.

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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.

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Yeah a simple blast can do it.

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