[Biopython] Converting transcript coordinates to genome coordinates

[Gerard Schaafsma]

Hi,

Did you have a look at https://mutalyzer.nl ? There is a position 
converter in there.

Best,

Gerard


On 05/07/17 12:04, Michiel de Hoon wrote:
> Dear all,
>
> Does anybody have some code to convert transcript coordinates to 
> genome coordinates?
> I have the position of a nucleotide along a transcript, and the genome 
> coordinates of the start and end of each exon in the transcript, and I 
> would like to find the position of the nucleotide in genome coordinates.
> Ideally, I am looking for some code that can find the genome 
> coordinates of a sequence of nucleotides.
> For example, if these are the exons:
> exon1  10000 10030
> exon2 10050 10080
> and a nucleotide sequence starting at position 20 and ending at 
> position 50 in transcript coordinates,
> then I am looking for the genome coordinates (10020,10030), (10050,10070).
>
> Thanks,
> -Michiel
>
>
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-- 
Gerard C.P. Schaafsma
Protein Structure and Bioinformatics Group
Dept. of Experimental Medical Science
Lund University
BMC B13, Hs 66
221 84 Lund
Sweden

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