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Hmmer again - #41

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AbhirupaGhosh wants to merge 17 commits into
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hmmer-again
Open

Hmmer again#41
AbhirupaGhosh wants to merge 17 commits into
mainfrom
hmmer-again

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@AbhirupaGhosh

@AbhirupaGhosh AbhirupaGhosh commented Jul 31, 2026

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Description

What kind of change(s) are included?

  • Feature (adds or updates new capabilities)
  • Bug fix (fixes an issue).
  • Enhancement (adds functionality).
  • Breaking change (these changes would cause existing functionality to not work as expected).

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Please ensure that all boxes are checked before indicating that this pull request is ready for review.

  • I have read and followed the CONTRIBUTING.md guidelines.
  • I have searched for existing content to ensure this is not a duplicate.
  • I have performed a self-review of these additions (including spelling, grammar, and related).
  • I have added comments to my code to help provide understanding.
  • I have added a test which covers the code changes found within this PR.
  • I have deleted all non-relevant text in this pull request template.
  • Reviewer assignment: Tag a relevant team member to review and approve the changes.

@AbhirupaGhosh AbhirupaGhosh self-assigned this Jul 31, 2026
@AbhirupaGhosh
AbhirupaGhosh marked this pull request as ready for review August 5, 2026 00:00
@AbhirupaGhosh

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If you have your favorite bug's duckdb (with protein_cluster_seq table), use that to try
.runHMMER() and .defenseHMMER()

@AbhirupaGhosh

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@epbrenner and @jananiravi, currently, we are not using any cut-off for evalue. The default is E <= 10. I think 1e-3 or a stringency like 1e-5 cut-off would make more sense. Let me know your thoughts.
Otherwise, the PR is again ready for your review.

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