songlab-cal / slc22a5

Variant effect prediction for SLC22A5 transporter gene using Potts models

slc22a5

Variant effect prediction for SLC22A5 transporter gene using Potts models.

Colabs

Predicting single mutant variant effects with trained potts models slc22a5_single_mutants.ipynb

Training a potts model from an alignment slc22a5_train_potts.ipynb

Data

Wildtype

wget http://s3.amazonaws.com/songlabdata/slc22a5/O76082.fasta

Alignments

wget http://s3.amazonaws.com/songlabdata/slc22a5/alignments/deepsequence.a3m
wget http://s3.amazonaws.com/songlabdata/slc22a5/alignments/eve.a3m
wget http://s3.amazonaws.com/songlabdata/slc22a5/alignments/hhblits.a3m
wget http://s3.amazonaws.com/songlabdata/slc22a5/alignments/mammals_30.a3m
wget http://s3.amazonaws.com/songlabdata/slc22a5/alignments/vertebrates_100.a3m

Trained Potts models

wget http://s3.amazonaws.com/songlabdata/slc22a5/potts/deepsequence.npz
wget http://s3.amazonaws.com/songlabdata/slc22a5/potts/eve.npz
wget http://s3.amazonaws.com/songlabdata/slc22a5/potts/hhblits.npz
wget http://s3.amazonaws.com/songlabdata/slc22a5/potts/mammals_30.npz
wget http://s3.amazonaws.com/songlabdata/slc22a5/potts/vertebrates_100.npz