https://github.com/ucl/cath-gemma
GeMMA, the step of the FunFam protocol that builds a superfamily's tree from S90 clusters of its Gene3D sequences
https://github.com/ucl/cath-gemma
cath function funfam gemma gene3d protein sequence
Last synced: 26 days ago
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GeMMA, the step of the FunFam protocol that builds a superfamily's tree from S90 clusters of its Gene3D sequences
- Host: GitHub
- URL: https://github.com/ucl/cath-gemma
- Owner: UCL
- Created: 2017-01-19T15:47:43.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2023-05-03T09:35:23.000Z (almost 2 years ago)
- Last Synced: 2024-06-06T12:37:53.246Z (11 months ago)
- Topics: cath, function, funfam, gemma, gene3d, protein, sequence
- Language: Perl
- Homepage:
- Size: 39.1 MB
- Stars: 1
- Watchers: 9
- Forks: 0
- Open Issues: 6
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Metadata Files:
- Readme: README.md
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README
**CATH-eMMA**
==========
Overview
---------
Fork of CATH-Gemma switching the core from HHsuite to embeddings or structural distances.
Main features/wishlist
- Revised protocol to use MMseqs2 instead of CD-HIT.
- Wrap pipeline in Python
- Add flags to use either embedding distances or 1/bitscore distances from Foldseek.
- Create infrastructure for multiple iterations (MARC)
- Create partitions using MDAs
This repo is part of the FunFams pipeline as an intermediate step before FunFHMMER.
The master FunFams repo is https://github.com/UCL/cath-funfam
See the GeMMA [Wiki](https://github.com/UCL/cath-gemma/wiki) for documentation (to expand with new usage).