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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
📦 A Command Line Tool for downloading protein structures, sequences and MSAs
Scripts to calculate sequence similarity networks (SSNs) and clustering of protein sequences.
PFAM's micro service to assist to Mistic2.
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. One of the advantages of this package is the easy switch to other databases by translation of accession numbers. All of these features enable to make a detailed analysis of proteins or RNA families and deal with large datasets.
Interactively explore the relationship between a variant of interest, protein structure, and previously reported variants.
Method for retrieving and visualising the protein domains of any protein coding isoform and of different genomes. Enables joint visualisations representing alternative splicing events.
A deepchain-app to predict protein family :microscope:
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.
Mapping domain co-occurrence networks with emphasis on c-d-GMP binding domains.
Snakemake pipeline for searching genomic sequences for those encoding proteins containing domains of choice
Minimal benchmark test to compare zstd (zstandard) compression with gzip for the datafile Pfam-A.full.gz
The script will generate and display the phylogeny tree, with MSA and domain distribution labels assigned to the tree leaves.