cfoldseeker
Welcome to cfoldseeker’s documentation!
cfoldseeker: Identify gene clusters using protein structure similarity.
cfoldseeker brings protein structure similarity to gene cluster mining! Starting from a query gene cluster of which you have all protein structure models, cfoldseeker searches all genomically colocalised structural homologs in a protein structure database.
The remote mode leverages the FoldSeek webserver to search against the AlphaFoldDB, and uses several cross-referencing APIs (UniProt ID mapping, KEGG, ENA GenPept) to retrieve the genomic location of every hit.
The local mode launches FoldSeek searches against a local structure database, and uses a genomic context database prepared from your sequences using its helper tool cfoldseeker-cds.
The local-clustered mode facilitates searches against huge structure databases by searching against the representative proteins of a target database preclustered with mmseqs2.
If you find cfoldseeker useful, please cite:
In preparation
User Guide
Comprehensive documentation for all API exposed by cfoldseeker:
API Reference