Pulldown mode with the whole mouse genome as candidate file

[PatriciaGimeno]

Hello,

I want to run the second step of AlphaPulldown. I have three mouse proteins of interest (baits) and I want to see their interactions against the rest of the mouse genome features. I have downloaded these features following the instructions at the end of the AlphaPulldown manual. I was wondering if there was a way of creating the candidates.txt file without manually having to add the name of each pkl file for the mouse genome?

Hope you can let me know.
Thanks!
Patricia

[DimaMolod]

Hi Patricia,
I think you can download the whole mouse proteome from uniprot (Download one protein sequence per gene (FASTA)):
Alternatively, just run this command:
mc ls embl/alphapulldown/input_features/Mus_musculus | grep ".pkl.xz" | awk '{print $NF}' | sed 's/.pkl.xz//'
Hope this helps,
Dima

[jkosinski]

Hi @PatriciaGimeno - we just noticed that the MSA features in this database do not include information necessary for pairing sequences from the same species, which may result in reduced accuracy. We are working on fixing this. While it should be fine for most of the cases, you may want to wait until we fix it.

[PatriciaGimeno]

Hi @jkosinski ,
Thank you for the heads up!
I will wait till it's fixed then to continue my simulations.

Please let me know when it has been fixed, thanks!
Kind regards,
Patricia