genome annotation [sstart] [send] – how to get protein sequence from gene

genome annotation [sstart] [send] – how to get protein sequence from gene

0

Hi,

I have a bacterial chromosome. I am struggling to understand how I can get protein sequences from genes annotated in the following way:

bacterial_chromosome_9_515

where sstart = 9 and send = 515

This is actually fine, as I can index the forward sequence using biopython:

faa = fasta[sstart:send].seq.translate(table=11)

However, when a gene is annotated in the reverse way, where sstart > send:

bacterial_chromosome_2423_1891

I am unsure how to get the corresponding protein sequence.

It would be much appreciated if someone could explain this.

Many thanks,

Dan


genome


annotation

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