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refresh-bio /FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

bioinformatics proteomics longest-common-subsequence pfam multiple-sequence-alignment sequence-similarity guide-tree

UpdatedSep 18, 2024
C++

diegozea /MIToS.jl

A Julia package to analyze protein sequences, structures, and evolutionary information

bioinformatics biology proteins pdb protein-structure julia-language conservation mutual-information structural-bioinformatics protein-evolution pfam sifts multiple-sequence-alignment coevolution protein-sequence-analysis

UpdatedOct 23, 2024
Julia

biomadeira /BioDownloader

📦 A Command Line Tool for downloading protein structures, sequences and MSAs

cli bioinformatics pdb fasta cath mmcif gff pfam sifts

UpdatedNov 21, 2017
Python

tderond /CO-ED

Co-occurrence of enzyme domains

bioinformatics enzyme domains gene-annotation uniprot pfam pfam-annotation

UpdatedSep 16, 2020
Jupyter Notebook

bateman-research /clustering-ssn

Scripts to calculate sequence similarity networks (SSNs) and clustering of protein sequences.

bioinformatics protein-sequence pfam protein-clustering

UpdatedMay 14, 2021
R

ecolell /pfamserver

PFAM's micro service to assist to Mistic2.

bioinformatics proteins pdb protein-structure pfam multiple-sequence-alignment protein-sequence-analysis

UpdatedFeb 15, 2023
Python

rubenchazarra /Transcript-Protein-Domain-Mapper

Method for retrieving and visualising the protein domains of any protein coding isoform and of different genomes. Enables joint visualisations representing alternative splicing events.

bioinformatics alternative-splicing pfam functional-consequences-splicing

UpdatedApr 14, 2022
R

pearcetm /jsproteinmapper

Interactively explore the relationship between a variant of interest, protein structure, and previously reported variants.

widget genomics interactive protein-structure data-visualization pfam jsproteinmapper-widget

UpdatedApr 17, 2019
JavaScript

cossio /Pfam.jl

Julia package to interact with the Pfam database.

UpdatedSep 2, 2024
Julia

theomeb /deepchain-app-pfam-32.0

A deepchain-app to predict protein family 🔬

nlp embeddings protein pfam protbert-model

UpdatedMay 12, 2021
Jupyter Notebook

mmalejky /proteins

Set of tools for protein sequence enrichment and protein domain finding

biopython protein-sequences blast sequence-alignment pfam fisher-test

UpdatedJun 1, 2022
Python

JuliaGol /PARS

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. …

bioinformatics pfam rfam

UpdatedJan 1, 2023
Python

HrishiDhondge /CroMaSt

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.

data-integration cath protein-domains pfam domain-databases

UpdatedJun 20, 2023
Common Workflow Language

Daniel-Ze /NLRextract

Find NLR hmms in protein sequences.

open-source open-science hmmer nlr pfam

UpdatedApr 10, 2024
Shell

suecharo /CPFF

keras bioinfomatics hmmer pfam bioinformatics-tool

UpdatedNov 8, 2018
Python

bio2bel /pfam

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

terminology biological-expression-language pfam protein-families

UpdatedNov 13, 2019
Python

MuthusaravananS /phylogeny-tree-with-MSA-and-Domain

The script will generate and display the phylogeny tree, with MSA and domain distribution labels assigned to the tree leaves.

python protein-sequences phylogeny msa ete3 pfam

UpdatedMay 22, 2023
Python

littleblackfish /c-di-GMP

Mapping domain co-occurrence networks with emphasis on c-d-GMP binding domains.

protein-domains pfam c-d-gmp

UpdatedMay 3, 2017
Jupyter Notebook

hamalcij /pfamannot

Protein Family Annotator

unix bioinformatics uniprot pfam protein-annotation

UpdatedMar 17, 2023
C

michalbukowski /pfam-genomes

Snakemake pipeline for searching genomic sequences for those that encode proteins containing domains of choice

snakemake proteins hmmer protein-sequence protein-domains pfam signalp

UpdatedSep 14, 2024
Python

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