Using API to Reproduce Figure 4(b): ISM for Alternative Allele

Help & Support
1

Hi AlphaGenome Team,

Thank you for your excellent work!

I am attempting to reproduce the ISM (In Silico Mutagenesis) plot shown in Figure 4(b) of your manuscript. Specifically, the ISM figure consists of two parts: the upper part can be easily reproduced using the score_ism_variants . However, this function does not support generating ISM results for alternative alleles, as the alternative bases are not present in the reference sequence.

I would like to know if the AlphaGenome API provides a straightforward method to reproduce the ISM analysis for alternative alleles as shown in the lower part of the figure.

Thank you for your assistance!

Best regards,

2

Hi @Zhao_Yang,

Thanks for the query, unfortunately this isn’t currently possible through score_ism_variants, though you can manually do this using score_variants by generating the set of variants via the ism_variants helper function.

We’ll look to try and add support for this in score_ism_variants in the future.

3

Hi @Zhao_Yang,

We have now added support for alternate allele ISM with this commit. The description also has a reproduction of Figure 4(b) :smiley:

Hope this is useful for your research!