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.

If an insertion or deletion results in different sequence lengths, is it necessary to pad with 'N’s beforehand? Or does Alphagenome have other handling logic, particularly during visualization?

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	1864	August 5, 2025
Uploading sequences to AlphaGenome Help & Support	5	2014	July 17, 2025
Can AlphaGenome predict the effect of an entire haplotype? Help & Support	1	1074	August 13, 2025
Multiple Deletions Help & Support	1	192	February 6, 2026
DNA methylation data for gene expression prediction Feedback & Feature Requests	2	337	March 2, 2026

Support for Multi-Base Mutations in AlphaGenome

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