homology-search

🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

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.

📈 Using structure information only for protein homology detection (IEEE BIBM 2024).

Smith-Waterman dynamic programming algorithm finding exact optimal local alignment motifs, homologous domains, and substrings across DNA and protein sequences.

Needleman-Wunsch dynamic programming algorithm for optimal global pairwise alignment of nucleotide and amino acid sequences with customizable scoring matrices.

Needleman-Wunsch dynamic programming algorithm for optimal global pairwise alignment of nucleotide and amino acid sequences with customizable scoring matrices.

Algebraic topology based header only library to extract insight of complex high dimensional data.

Smith-Waterman dynamic programming algorithm finding exact optimal local alignment motifs, homologous domains, and substrings across DNA and protein sequences.

Native Smith–Waterman homology in Rust that is fast, sensitive, low-memory, and highly scalable

Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.

A seed-based homology searching tool

GWIscan is a pipeline for the genome-wide identification and in silico characterization of gene families.

A Nextflow workflow for scalable distributed taxonomy-enabled NCBI Blast and Diamond homology searches

A snakemake workflow for iterative sequence profile searching using jackhmmer from the HMMer3 package.

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.

Reproducible, one-command HMM-based homologue discovery for protein families across phage/viral databases (six-frame search, ORF validation, iterative convergence). macOS/Linux; Windows via WSL2.

A simple pipeline to create and search HMM models against reference protein databases.