Question about example data

[oatml]

Question about example data

[pascalnotin]

Dear Nan,

Thank you for taking an interest in our work and sorry for the slow response.

Regarding your first question: yes, you are right about the jackhmmer flags. The PTEN file you are referring to is a preprocessed file. We have now added:

• additional MSA examples in the github repo (https://github.com/OATML-Markslab/EVE/tree/master/data/MSA)
• a more detailed description of this process in the README file (https://github.com/OATML-Markslab/EVE/blob/master/README.md#msa-creation)
  We have also made all multiple sequence alignments available for download from our website evemodel.org. Please let us know if this does not fully address your question.

Regarding your second question: the condition used in the jackhmmer search is not that every sequence has Lcov* >= 0.7L., but rather that each sequence has Lcov* >= 0.5L. The way we obtained our multiple sequence alignments was to run jackhmmer for a range of bitscore thresholds. Then given multiple options, we pick one based on criteria relating to coverage and number of sequences in the alignment. You are correct that the number of sequences in the alignment being greater than 10L is a lower priority than Lcov >= 0.7L.

Finally, please note we have moved the official repo to the following address: https://github.com/OATML-Markslab/EVE.

Best regards,
The EVE team