protein-families

showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.

Generation and updating of protein families

Workflow for identifying and classifying homologous gene/protein sequences

Build protein families from sequence clusters by iterative HMM search over very large databases — streaming, deterministic, pyHMMER-based.

An R Package for characterizing proteins using molecular evolution and phylogeny

Multi-label protein function annotation

Efficient search of complex motifs in kmer space

Pipeline to generate MGnifams --metagenomics derived protein families from MGnify Proteins database

Sample known protein families and benchmark how well they can be reconstructed by protein-family generation methods.

Scripts and datasets supporting FunVar TCGA/TRACERx Functional Impact Event (FIE) scoring and related analyses.

Understanding the relationship between amino acid sequence and protein function is a long-standing problem in molecular biology with far-reaching scientific implications.

A Bio2BEL package for converting InterPro to BEL

The entire Pfam universe as an on-device inference engine: paste a sequence, get a family, offline. Swift/SwiftUI for iOS, iPadOS, macOS, visionOS and watchOS.

A Bio2BEL package for PFAM (https://pfam.xfam.org/)

Convert FamPlex to BEL

A Bio2BEL package for converting ExPASy to BEL

DPCexplorer: An open-science, browser-based web application built with Django for the interactive exploration, search, and visualization of sequence-based (DPCfam) and structure-based (DPCstruct) protein domain metaclusters.

DPCexplorer: An open-science, browser-based web application built with Django for the interactive exploration, search, and visualization of sequence-based (DPCfam) and structure-based (DPCstruct) protein domain metaclusters.