Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
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Updated
Apr 29, 2024 - C
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
Find NLR hmms in protein sequences.
Mutual Information Tools for protein Sequence analysis in Julia
Snakemake pipeline for searching genomic sequences for those encoding proteins containing domains of choice
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.
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. …
Set of tools for protein sequence enrichment and protein domain finding
Method for retrieving and visualising the protein domains of any protein coding isoform and of different genomes. Enables joint visualisations representing alternative splicing events.
Scripts to calculate sequence similarity networks (SSNs) and clustering of protein sequences.
A deepchain-app to predict protein family 🔬
Co-occurrence of enzyme domains
Minimal benchmark test to compare zstd (zstandard) compression with gzip for the datafile Pfam-A.full.gz
A Bio2BEL package for PFAM (https://pfam.xfam.org/)
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