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 location…

I think your question is related to these two threads: Can AlphaGenome predict the effect of an entire haplotype? - #2 by tward Using AlphaGenome to predict the cooperativity of multiple SNPs? - #7 by Steve_S

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.

Support for Multi-Base Mutations in AlphaGenome

Feedback & Feature Requests

Claus_Volko September 1, 2025, 6:58am 2

I think your question is related to these two threads:

Can AlphaGenome predict the effect of an entire haplotype? - #2 by tward
Using AlphaGenome to predict the cooperativity of multiple SNPs? - #7 by Steve_S

Topic		Replies	Views
Using AlphaGenome to predict the cooperativity of multiple SNPs? Community	6	1789	August 5, 2025
Can AlphaGenome predict the effect of an entire haplotype? Help & Support	1	1031	August 13, 2025
Uploading sequences to AlphaGenome Help & Support	5	1979	July 17, 2025
Multiple Deletions Help & Support	1	169	February 6, 2026
DNA methylation data for gene expression prediction Feedback & Feature Requests	2	278	March 2, 2026

Support for Multi-Base Mutations in AlphaGenome

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