§ 06 · domain
Functional Genomics & Variant Effect
Regulatory genomics & expression prediction
4 tools
Borzoi
Calico
successor to Enformer with better long-range performance.
ChromBPNet
chromatin state prediction.
Enformer
DeepMind
predicts gene expression from sequence; long-range (~100kb) interactions.
Sei
chromatin state prediction.
Splicing
2 tools
Pangolin
splice site prediction; clinically used for variant interpretation.
SpliceAI
splice site prediction; clinically used for variant interpretation.
Variant effect prediction
6 tools
AlphaMissense
DeepMind
classifies missense variants as benign/pathogenic across the human proteome.
ESM-1v
zero-shot variant effect via PLM likelihood scoring.
ESM-2
zero-shot variant effect via PLM likelihood scoring.
EVE
alternative approaches.
Evo 2
Arc Institute
variant effect across DNA, RNA, and protein in a single model.
PrimateAI-3D
alternative approaches.