I have a series of 15bp DNA sequences from single-cell barcodes and I would like to encode them into a shorter than 15 digits number so that each unique 15bp DNA sequence will create a unique numeric value. What's the best way of achieving this?


1 Answer 1


What you are asking is called a "hash" (wiki).

In python, get your oligo as a string and use the standard library method hash(oligo), this is a number that gets used for a lot of operations. It is however always a 18+1 digit number in decimal, so a different solution is needed.

There are four nucleobases, so binary conversion from scratch is easy and best option and each solution will be unique and small. Each base takes up 2 bits and you concatenate these and convert them to hex or decimal —the length should be 10 decimal digits. One issue is when you have a oligo of a different length which start with adenosine or not.

One issue with this is the order. I am not sure where it comes from but the bases are nearly often expressed in the order ATGC. So...

mapping = {'A': '00', 'T': '01', 'G': '10', 'C': '11'}

It is satisfying how the first digit is the W/S, while the second is R/Y.

Now simply covert and add them compressed = functools.reduce(lambda acc,base : acc+mapping[base], oligo, '') and covert the string to decimal like so int(compressed, 2).

  • $\begingroup$ The problem is hash collisions, there is no guarantee that the compression is unique $\endgroup$ Commented Jun 19, 2020 at 14:41
  • $\begingroup$ Hash collision with the fake-hash would happen with two oligos that are the same but one has one or more extra adenosines. The oligo was said to be 15bp, so this does not apply. A workaround is to add a 1 at the start... $\endgroup$ Commented Jun 19, 2020 at 15:00

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.