Support for Multi-Base Mutations in AlphaGenome

Feedback & Feature Requests
1

Hey,

I wanted to ask if, instead of introducing single-nucleotide variations and checking their effects on the signal using dna_model.predict_variant() — which has been very useful — does AlphaGenome also support mutating entire segments of nucleotides, it could be one location or several locations?

For example, is it possible to modify a 20 bp sequence, at one location or potentially at multiple locations, and then analyse the resulting impact on the signal? If so, how can this be done?

Thanks!

2

I think your question is related to these two threads:

3

It might be possible. If you construct the reference allele and alternative allele to be the same length, but include the multiple SNPs you’d like to predict. e.g. ATTGCA>GTTACT, which include 3 SNPs. Please feel free to share any feedback if this works for you.