Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval
🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
RNAlien - unsupervised RNA family model construction
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
Algebraic topology based header only library to extract insight of complex high dimensional data.
📈 Using structure information only for protein homology detection (IEEE BIBM 2024).
Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.
A seed-based homology searching tool
A snakemake workflow for iterative sequence profile searching using jackhmmer from the HMMer3 package.
Searching proteins against a database of embeddings
A simple pipeline to create and search HMM models against reference protein databases.
This repository contains a set of scripts and workflows designed to search for Respiratory Complex I (NADH Ubiquinone Oxidoreductase) subunits in prokaryotic genomes and proteomes.
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