protein position to nucleotide position

Question

[MAK]

I have translated a complete genome in the six frames then I got a start and stop position for a gene on this translated genome.

Now I need to compare these coordinates to nucleotide positions:

if I am in same positive strand what I thought of is:

if frame 1: nuc_start=prot_start*3

if frame 2: nuc_start=prot_start*3+1

if frame 3 nuc_start =prot_start*3+2

Question: Am I right? And what about the other strand frames?

Answer 1

[Devon Ryan]

Assuming you want 1-based coordinates, then you would instead want:

frame 1: nuc_start = 3*(prot_start-1)+1
frame 2: nuc_start = 3*(prot_start-1)+2
frame 3: nuc_start = 3*(prot_start-1)+3

This assumes that you simply ignore the first 2 bases when translating frame 3, rather than padding the translated sequence with something.

It works the same for the other strands, how you do the math will depend on whether you reversed the sequence or not. If you reversed things, then the resulting coordinates will be from the end of the chromosome/contig. Also, frame -1 will be dealt with the same as frame +3 and -3 the same as +1.

If this is unclear, draw out a short sequence, how this works should be apparent then.

Edit: And as Pierre pointed out, this all assumes that there's no splicing...

[MAK]

Yes I translated the reverse complement for the other strand frames, I couldn't figure out how the frame -3 is dealt same as +1 and vice versa

[Devon Ryan]

The "also" was incorrect in that sentence. Just calculate the position as if you were on the + strand and the subtract that from one more then the chromosome/contig length.

Answer 2

[Pierre Lindenbaum]

Am I right ?

No: https://en.wikipedia.org/wiki/RNA_splicing

See also: Amino Acid Change To Genomic Location

[MAK]

I assume there is no splicing