Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
A Julia package to analyze protein sequences, structures, and evolutionary information
Co-occurrence of enzyme domains
Scripts to calculate sequence similarity networks (SSNs) and clustering of protein sequences.
PFAM's micro service to assist to Mistic2.
A deepchain-app to predict protein family 🔬
Method for retrieving and visualising the protein domains of any protein coding isoform and of different genomes. Enables joint visualisations representing alternative splicing events.
CroMaSt (Cross Mapper of domain Structural instances) is an automated iterative workflow to clarify domain definition by cross-mapping of domain structural instances between domain databases.
Interactively explore the relationship between a variant of interest, protein structure, and previously reported variants.
Command-line bioinformatics tools and utilities
Set of tools for protein sequence enrichment and protein domain finding
PARS is a python package for browsing and downloading files deposed in Pfam and Rfam databases (e.g. sequences, alignments, hmm). It has implemented classes dedicated to Pfam data like: PfamFamily or PfamClan. PARS is compatible with Biopython modules, but also is extended by HMMER wrapper which enables convenient usage of downloaded HMM files. …
Annotate PICRUSt2 functional IDs (KO, EC, Pfam, etc.) using description mapfiles
Find NLR hmms in protein sequences.
Mapping domain co-occurrence networks with emphasis on c-d-GMP binding domains.
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