protein-domains

There are 2 repositories under protein-domains topic.

LKremer / showTree
showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.
gene-families protein-families ete3 python protein-domains phylogenetic-trees phylogenetics visualization treeview
Language:Python 30
thekaplanlab / msabrowser
🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
msabrowser msa-viewer sequence-alignment-visualization multiple-sequence-alignment protein-domains msa bioinformatics genetics sequence-alignment
Language:JavaScript 30
SWORD2
DSIMB / SWORD2
SWift and Optimized Recognition of protein Domains
protein-structure protein-domains protein-units proteins protein-junctions
Language:Perl 23
evocellnet / ptm_hotspots
Estimate PTM hotspots in protein sequence alignments
bioinformatics phosphoproteomics protein-domains
Language:Python 13
sib-swiss / pftools3
A suite of tools to build and search generalized profiles
profile protein-domains motif sequence-analysis
Language:C 9
cmbi / metadome
MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their mutation of interest in the context of general population-based genetic variation and provide detailed information of pathogenic variants found across homologous domain positions.
genes genetics proteins protein-domains genetic-tolerance domain-homology pathogenicity pathogenic-variants variant-annotations variant-interpretation gene-annotation protein-annotation
Language:Python 6
lafita / tadoss
:open_hands: TADOSS: TAndem DOmain Swap Stability predictor
bioinformatics protein-domains protein-structure protein-aggregation proteins
Language:Python 6
CSB-KUL / yMap
An automated method to map yeast variants to proteins modifications and functional regions
systems-biology mutated-proteins protein-protein-interaction protein-modification protein-structure protein-domains yeast python
Language:Python 5
BIONF / FAS
FAS - Tool for Feature Architecture Similarity calculation
feature-architectures protein-comparison protein-domains proteins
Language:Python 4
damianosmel / dom2vec
dom2vec: Protein domain embeddings
bioinformatics protein-domains protein-domain-architectures embeddings
Language:Python 4
sinc-lab / Comparison-of-Protein-learning
Comparison of protein learning
protein sequence protein-sequences protein-sequence proteins homo-sapiens human-protein geneontology gene-ontology protein-domains blast embeddings
Language:Jupyter Notebook 4
ISYSLAB-HUST / Res-Dom
protein domain prediction
deep-learning protein protein-domains
Language:Python 2
ostrokach / uniparc_xml_parser
UniParc dataset describing ~300 million protein sequences converted into relational tables accessible through Google BigQuery (and as Parquet files).
bioinformatics protein-sequences protein-domains bigquery parquet-files csv-files
Language:Rust 2
profile-HMM-protein-seq
espositomario / profile-HMM-protein-seq
Profile hidden Markov model (HMM) to identify the Kunitz domain in protein sequences, using MSA-guided training and optimization.
hmm protein-domains structural-biology hidden-markov-model protein-sequences uniprot
Language:Python 1
furacca / cuterle
THIS PROJECT IS NO LONGER SUPPORTED See Brivez Instead!! https://github.com/furacca/brivez/ - ------------------------------------------ - Cuterle is a bioinformatic tool which return an output file containing every domain annotated by InterProScan via Pfam or SMART analysis from the list of protein submitted.
bioinformatics-tool fasta interpro interproscan protein protein-domains protein-sequence-analysis python3 tsv turtle-graphics
Language:Python 1
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.
cath data-integration pfam protein-domains domain-databases
Language:Common Workflow Language 1
NCBI-Codeathons / Domain_HMM_Boundaries
Refining Domain Boundaries and Performing Large Scale Parsing
ncbi-virus-discovery-2 metagenomics protein-domains viruses contigs bioinformatics bioinformatics-pipeline
Language:Jupyter Notebook 1
psipred / dompred
Protein sequence domain predictor
protein-structure protein-domains
Language:Perl 1
bio2bel / interpro
A Bio2BEL package for converting InterPro to BEL
biological-expression-language systems-biology networks-biology protein-families proteins protein-domains interpro
Language:Python 0
furacca / brivez
Brivez is a bioinformatic tool thought as Quality of Life's improvement, providing high quantity of data in a snap, giving you a quick view on what you could find inside your transcriptome/sequences' list.
bash-script bioinformatic-tools deepsig fasta hmmer3 protein protein-domains python3 transcriptome transcriptome-analysis
Language:Python 0
littleblackfish / c-di-GMP
Mapping domain co-occurrence networks with emphasis on c-d-GMP binding domains.
pfam c-d-gmp protein-domains
Language:Jupyter Notebook 0
michalbukowski / pfam-genomes
Snakemake pipeline for searching genomic sequences for those encoding proteins containing domains of choice
hmmer pfam protein-domains protein-sequence proteins signalp snakemake
Language:Python 0
pmastrogiovanni / kunitz_hmm
HMM protein domain prediction
hmm protein-domains
Language:Jupyter Notebook 0
uds-helms / MutaNET
Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.
ngs mutations automated-analysis gene-regulatory-networks pipeline mutation-analysis converters protein-domains ngs-pipeline coding-regions transcription-factor-binding-site gui
Language:Python 0
victoria-r / BLASTandTransdecoder
Using BLAST and Transdecoder.
bioinformatics blast hmmscan profile-hmm protein-domains swissprot transdecoder trinity blastp bash
Language:Shell 0
almeidasilvaf / planttfhunter
An R package to identify plant transcription factors from protein sequence data and classify them in families
rstats transcription-factors protein-domains gene-families functional-genomics hidden-markov-models plant-genomics plants
Language:R

protein-domains

LKremer / showTree

thekaplanlab / msabrowser

DSIMB / SWORD2

evocellnet / ptm_hotspots

sib-swiss / pftools3

cmbi / metadome

lafita / tadoss

CSB-KUL / yMap

BIONF / FAS

damianosmel / dom2vec

sinc-lab / Comparison-of-Protein-learning

ISYSLAB-HUST / Res-Dom

ostrokach / uniparc_xml_parser

espositomario / profile-HMM-protein-seq

furacca / cuterle

HrishiDhondge / CroMaSt

NCBI-Codeathons / Domain_HMM_Boundaries

psipred / dompred

bio2bel / interpro

furacca / brivez

littleblackfish / c-di-GMP

michalbukowski / pfam-genomes

pmastrogiovanni / kunitz_hmm

uds-helms / MutaNET

victoria-r / BLASTandTransdecoder

almeidasilvaf / planttfhunter