| ColabFold |
Structure Prediction |
Uses AF2, AF2-multimer and Rosettafold for protein structure preditcition |
Protein sequence |
PDB,numpy array, jsoin |
Jupyter notebook on google servers |
|
Browser |
Browser/Python |
Colabfold uses google colab notebooks to run different versions of
Alphafold2 for structure prediction of monomers and protein complexes. The
multiple sequence alignment (MSA) step is performed by using mmseqs API (see
below) and can be used to generate MSAs for other puproses. There are many
different versions of AF2 are available. Due to limitations in available
hardware in free tier google colab notebooks it may not be feasible to fold
proteins or complexes >2000 aa total.
|
Easy to use, no gpu or sophisticated hardware needed |
Limited to GPUs available on free tier for google colab. This will limit the size of
the protein (or protein complexes) that can be predicted.
|
|
|
https://github.com/sokrypton/ColabFold
|
N/A |
|
Yes |
| VEP |
Variant effect
prediction
|
Determines effects of variants |
VCF / Variant
information manually entered
|
VEP Format TSV |
Web and Command Line |
Apache 2.0 |
Mac / Windows / Linux |
Unix / Web |
VEP is Ensembl’s variant effect predictor. It integrates most common variant
annotation tools and databases in a single location. It is available as a
command line tool and a web interface for a smaller subset of variants. The
command line tool is installed (with numerous annotation packages) in HPC and
is available for all users. Many variant effect prediction tools like
AlphaMissense, spliceai and MTSplice are readily integrated into VEP and can
be added to variant annotations.
|
Has a lot of tools already integrated
and can be called with simple flags. The output format can be specified for
easy parsing (vcf, txt, json).
|
Not all tools are available online,
the hpc modules will require command line interaction. Depending on the
modules needed can be somewhat slow.
|
Detailed documentation and
tutorials
|
https://www.ensembl.info/
|
https://useast.ensembl.org/info/docs/tools/vep/index.html
|
Many Organisms |
|
No |
| MMSeqs |
Sequence alignment |
MMSeqs server can only be accessed through colabfold at the momente but a
local server can also be set up if needed
|
|
|
|
|
|
API call |
MMSeqs is a rapid multiple sequence alignment tool. It is several orders of
magnitude faster than hmmer and jackhmmer with similar accuracy. Currently
the web server is not available for use but you can still use mmseqs through
colabfold (see above).
|
Very fast, can generate sequecne alignments and clusters from 1000s organisms. |
Can only be accessed through colabford or through an API. |
|
|
https://search.mmseqs.com/
|
Many Organisms |
|
No |
| Expasy Tools |
General tools |
Simple calculations for protein, DNA, RNA sequence analysis |
Sequence |
Depends on tool used |
Web and Command Line |
Depends on tool used |
Mac / Windows / Linux |
Unix / Web |
Expasy is hosted by Swill Bioinformatics Resource Portal. This is not a
single tool but a large collection of small tools that can be use
independently from one another. There are several tools for sequence,
structure and small molecule analysis from similarity searches to simple
molecular weight/isoelectric point calculation. Each tool has its own web
interface with detailed documentation.
|
Very easy to use and
diverse tools on many different types of
analysis.
|
These are small tools
that are designed to perform quick calculations.
There is no API for programmatic acccess.
|
|
|
https://www.expasy.org/
|
N/A |
|
No |
| Alphafold 3
Server
|
Structure Prediction |
Structure Prediction |
Sequence |
Zipped download + Web
output
|
Web |
Non-commercial use only (See site for full terms) |
Browser |
Browser |
AlphaFold Server is a
web-service that can generate highly accurate
biomolecular structure predictions containing proteins, DNA, RNA, ligands,
ions, and also model chemical modifications for proteins and nucleic acids in
one platform. It’s powered by the newest AlphaFold 3 model. While AF3 is
publicly available pending agreement to certain license conditions the server
provides an easier to use alternative.
|
Easy to use, there
are no programming or hardware requiremnets.
Reasonably fast.
|
There are limilations
on the number of structures that can be calculated
and limitations on the types of questions that can be asked.
|
|
|
https://alphafoldserver.com/welcome
|
N/A |
|
No |
| Chai1 Server |
Structure Prediction |
Uses Chai model for structure prediction |
protein, DNA, RNA
sequence and smiles strings
|
pdb, json |
Web |
Non-commercial use only (See site for full terms) |
Browser |
Browser |
Chai1 is another protein, DNA, RNA, ligand structure
prediction tool that is
developed by Discoverly labs. Based on their technical reports it is as
accurate as Alphafold3 in most instances and shows better perfromance on
antibody-protein interactions. The model is available openly
in github and there is a web interface for ease of use.
|
Same as AF3 server |
Same as AF3 server |
About page |
|
https://lab.chaidiscovery.com/auth/login?callbackUrl=https%3A%2F%2Flab.chaidiscovery.com%2Fdashboard
|
N/A |
|
No |
| PhaSePred |
Protein
Characterization
|
Protein Characterization |
Protein Name / ID |
Web output /
downloadable results
|
Web |
free for non-commercial use for academic, government and non-profit
institutions
|
Browser |
Browser |
Phase separation (PS)
mediates the compartmentalization of proteins and
nucleic acids in cell. This process is driven by multivalent weak
interactions mediated by intrinsically disordered regions (IDRs) or multiple
modular domains. A difference between these two interactions is that a single
molecule species can undergo IDR-mediated phase separation, while phase
separation mediated by multiple interacting domains often involves two or
more different molecule species.
PhaSePred is a centralized resource that provides self-assembling and
partner-dependent phase-separating protein prediction and integrates scores
from several PS-related predicting tools.
|
Easy to use, quick
results, good visualization tools, focused on
phase separation
|
May not cover all
types of phase separation or complex interactions
|
Tutorial available on
site
|
No specific community forum |
http://predict.phasep.pro/
|
Primarily human |
|
No |
| DeepLoc |
Protein Localization Prediction |
Predicts subcellular localization of eukaryotic proteins using deep learning
models.
|
Protein Sequence in
FASTA format
|
Web output /
downloadable results
|
Web |
The downloadable version of DeepLoc 2.1 is being commercialized (it
is licensed for a fee to commercial users)
|
Browser |
Browser |
DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins.
DeepLoc 2.0 is a multi-label predictor, which means that is able to predict
one or more localizations for any given protein. It can differentiate between
10 different localizations: Nucleus, Cytoplasm, Extracellular, Mitochondrion,
Cell membrane, Endoplasmic reticulum, Chloroplast, Golgi apparatus,
Lysosome/Vacuole and Peroxisome. Additionally, DeepLoc 2.0 can predict the
presence of the sorting signal(s) that had an influence on the prediction of the
subcellular localization(s). One can use DeepLocPro for prokaryotic proteins
and DeepLocRNA for RNA localization.
|
High accuracy,
supports many localization types.
|
Limited to eukaryotic
proteins, performance may vary based on sequence
data quality.
|
Brief instructions
section
|
No specific community forum |
https://services.healthtech.dtu.dk/services/DeepLoc-2.1/
|
Eukaryotes |
|
No |
| Phobius |
Prediction |
Predicts transmembrane topology and signal peptides in proteins. |
Protein Sequence in
FASTA format
|
Web output /
downloadable results
|
Web |
Phobius is freely available for local installation for academic use |
Browser |
Browser |
Phobius is a tool
that predicts the transmembrane topology and
signal peptides of a protein from its amino acid sequence. It can identify
membrane, signal peptide, or cytoplasmic loop states with a single label. It
can also force the predictor to choose between two types of features to
improve discrimination. Phobius is available for free local installation for
academic use on Unix platforms with Perl version 5.6 or later. It can also be
accessed through the Phobius web server.
|
Accurate
transmembrane prediction, user-friendly interface
|
Primarily limited to
membrane proteins, not suitable for predicting
other structural features.
|
Instructions section |
No specific community forum |
https://phobius.sbc.su.se/index.html
|
Eukaryotes |
|
No |
| ProtVar |
Variant Annotation |
Provides information on the potential
functional impact of protein variants, particularly related to disease.
|
Genomic or Protein variant location |
Web output /
downloadable results
|
Web |
Creative Commons license |
Browser |
Browser |
ProtVar (Protein
Variation) is a resource to investigate SNV
missense variation (not InDels) in humans by presenting annotations which may
be relevant to interpretation. The tool is similar to VEP. It is easier to
use but not as robust as VEP (see above).
|
High relevance to
disease research, integrates multiple data sources
|
Primarily focused on
human data, limited to annotated variants
|
Webinar tutorial
video
|
No specific community forum |
https://www.ebi.ac.uk/ProtVar/
|
Primarily human |
|
No |
| GENCODE |
Genome database |
Provides comprehensive and high-quality annotations of human and mouse
genomes, including gene models and transcript variants.
|
No input |
GTF, GFF, FASTA |
Web |
Open (See: https://www.ebi.ac.uk/about/terms-of-use) |
Browser |
Browser |
GENCODE is a project that aims to identify and annotate all protein-coding
genes in the Human and Mouse genome, using a combination of computational
analysis, targeted experimental approaches and manual curation. GENCODE also
contains gene annotation files, amino acid and nucleotide sequence files of
known proteins and transcripts. The project releases updates to its database
multiple times per year and all data are available for download.
|
Actively updated |
Limited to human and mouse species, large
dataset may be cumbersome for some users.
|
Documentation on data output types |
Github Page |
https://www.gencodegenes.org/
|
Human and Mouse |
|
No |
| GTEx |
Expression database |
Provides gene expression data across different
tissues from healthy human donors to understand genetic regulation of gene
expression.
|
Gene ID / name |
Web output /
downloadable results
|
Web |
Open licensing (see: https://gtexportal.org/home/license) |
Browser |
Browser |
GTEx is the Adult Genotype Tissue Expression (GTEx) project and aims to study
human gene expression and regulation, and its relationship to genetic
variation across multiple diverse tissues and individuals. More specifically
GTEx contains data from and includes RNA-seq, snRNA-Seq, long-read RNA-seq,
QTL (single and multi-tissue), histology, protein expression, methylation
QTLs, and variant detections, across various tissue types and individuals.
These data can be downloaded locally or visualized in a browser. The online
browsers can be used to visualize bulk RNA-Seq expression, snRNA-Seq
expression and Tissue & Histology data. There is also dGTEx which aims to
study development-specific genetic effects on gene expression, as well as NHP
dGTEx which studies development-specific genetic effects on gene expression
in non-human primates. Both dGTEx and NHP dGTEx are still underway with no
data being released yet.
|
Rich resource for gene expression analysis
across tissues.
|
Data only from healthy donors, doesn’t cover
disease-specific data.
|
How to videos and tutorials |
Github Page |
https://gtexportal.org/home/
|
Human |
|
No |
| Alphafold
Database
|
Structure Prediction |
Provides predicted protein structures
generated by AlphaFold for a wide range of species.
|
Protein / Gene name or Protein sequence |
Web output / PDB
downloads
|
Web |
Creative Commons Attribution 4.0 |
Browser |
Browser |
Google DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI)
have partnered to create AlphaFold DB to make these predictions freely
available to the scientific community. The latest database release contains
over 200 million entries, providing broad coverage of UniProt (the standard
repository of protein sequences and annotations). They provide individual
downloads for the human proteome and for the proteomes of 47 other key
organisms important in research and global health.
|
State-of-the-art predictions, large-scale
coverage across species.
|
Models based on predictions, not experimental
data.
|
FAQ and About page |
Github and Google
Groups
|
https://alphafold.ebi.ac.uk/
|
48 complete proteomes
(including Human)
|
|
Yes |
| ESM Atlas |
Structure Database |
Provides a large-scale resource for protein
embeddings, using ESM (Evolutionary Scale Modeling) to predict protein
sequences and functions.
|
Protein Sequence in FASTA format |
Web output /
downloadable results
|
Web |
CC BY 4.0 license |
Browser |
Browser |
Predicts protein
properties, evolutionary embeddings
|
High-quality embeddings, useful for functional annotation. |
Focus on sequence-function relationships; may
not be fully predictive for all proteins.
|
About page for documentation |
Github Page |
https://esmatlas.com/
|
Eukaryotes |
|
No |
| Interpro |
Protein Function, Annotation |
Integrates diverse protein family, domain, and
functional site information to annotate protein sequences.
|
Protein Sequence in FASTA format / Protein ID |
Web output /
downloadable results
|
Web |
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. |
Browser |
Browser |
InterPro is a
database which contains functional analysis of
proteins and contains classification of protein families and predictions of
domains and sites. InterPro integrates different member databases into a
larger InterPro consortium, so searching for proteins can be aggregated
across all the databases. Users can search for proteins by sequence, protein
name or search for specific domain architectures of interest. Additionally,
data from entire proteomes or member databases can be exported locally.
|
Wide coverage of protein domains, integrates
well with other tools.
|
Somewhat complex interface for new users. |
Quick tour guides and documentation pages |
No specific community forum |
https://www.ebi.ac.uk/interpro/
|
Many Organisms |
|
Yes |
| STRING |
Protein-Protein Interaction |
Provides known and predicted protein-protein
interactions (PPIs) for a wide range of organisms.
|
Protein Name / ID |
Web output /
downloadable results
|
Web |
Creative Commons BY 4.0 license. |
Browser |
Browser |
STRING is a database of known and predicted protein-protein interactions. The
interactions include direct (physical) and indirect (functional)
associations; they stem from computational prediction, from knowledge
transfer between organisms, and from interactions aggregated from other
(primary) databases.
|
Rich network of interactions, integrates with
other databases.
|
Predictive data may not always be as reliable
as experimental data.
|
User documentation and help videos |
No specific community forum |
https://string-db.org/
|
Many Organisms |
|
No |
| PhospoSitePlus |
Post-translational Modifications (PTMs) |
Provides information on experimentally
verified phosphorylation sites, as well as other PTMs.
|
Protein Sequence in FASTA format / Protein ID |
Web output /
downloadable results
|
Web |
Licensing Agreement (see: https://www.phosphosite.org/staticLicensing) |
Browser |
Browser |
PhosphoSitePlus is an online database which contains data for the study of
protein post-translational modifications. PhosphoSitePlus contains data on
post-translational modifications such as phosphorylation, acetylation,
methylation, ubiquitination, and O-glycosylation. The database includes data
from various diseases, tissue types and cell lines as well as built in motif
analysis, sequence logo analysis and kinase predictions. Proteins can be
searched for uniquely or comparatively by sequence or various specific sites
and there are also options to download datasets locally. PhosphoSitePlus uses
publicly available data, from numerous journal articles that have been
published.
|
Extensive, experimental data on PTMs. |
Primarily focused on human data, may not cover
all PTMs comprehensively.
|
About page with broad overview of features |
No specific community forum |
https://www.phosphosite.org/homeAction.action
|
Human, mouse and rat |
|
No |
| DisProt |
Protein Structure, Disorder Prediction |
Database of intrinsically disordered proteins
(IDPs) and disordered regions within proteins.
|
Protein Sequence in FASTA format / Protein ID |
Web output /
downloadable results
|
Web |
Creative Commons Attribution 4.0 International License |
Browser |
Browser |
DisProt is the major
manually curated repository of Intrinsically
Disordered Proteins, both for structural and functional aspects. Expert
curators are involved in collecting experimentally confirmed biological data,
valuable for the scientific community, and for updating and maintaining
DisProt over time.
|
High-quality, experimentally verified data on
intrinsically disordered proteins.
|
Limited coverage compared to complete proteome
analysis; focuses on disordered regions only.
|
Courses offered virtually or in person + documentation page |
No specific community forum |
https://disprot.org/
|
Human and other model organisms |
|
No |
| VASTdb |
Alternative Splicing |
Alternative Splicing (AS) profiles
across multiple tissue and cell types
|
Gene IDs / Coordinates |
Web output /
downloadable results
|
Web |
Creative Commons License (Attribution-NonCommercial 4.0
International)
|
Browser |
Browser |
VastDB is a database of Alternative Splicing (AS) profiles across multiple
tissue and cell types. VastDB contains AS events (including cassette exons,
microexons, alternative 5′ and 3′ splice sites and retained introns) from
various species. AS event identification and sequence inclusion level
quantification in RNA-seq samples have been performed with VAST-TOOLS. In
addition to AS inclusion levels, Vas’d provides general information about the
AS events, including genomic and sequence context, impact on the reading
frame, overlap with protein domains and disordered regions, mapping to
protein structures, evolutionary conservation and primers for AS event
validation through RT-PCR. Moreover, it also provides measures of Gene
Expression, using the cRPKM metric.
|
Alternative Splicing (AS) profiles across multiple tissue and cell types |
Limited number of organisms |
FAQ page |
No specific community forum |
https://vastdb.crg.eu/wiki/Main_Page
|
Human, mouse, rat,
cow, chicken, zebrafish and fruit fly
|
|
No |
| BioGRID |
Protein-Protein Interactions |
Provides an interaction repository that
catalogs experimental data on protein-protein and genetic interactions across
multiple organisms.
|
Protein / Gene IDs |
Web output /
downloadable results
|
Web |
Open (see: https://wiki.thebiogrid.org/doku.php/terms_and_conditions) |
Browser |
Browser |
The Biological
General Repository for Interaction Datasets
(BioGRID) is a public database that archives and disseminates genetic and
protein interaction data from model organisms and humans (thebiogrid.org).
BioGRID currently holds over 1,740,000 interactions curated from both
high-throughput datasets and individual focused studies, as derived from over
70,000+ publications in the primary literature. Complete coverage of the
entire literature is maintained for budding yeast (S. cerevisiae), fission
yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand
curation across multiple metazoan species are underway.
|
Large dataset of experimentally verified
interactions, supports many organisms.
|
Limited to experimental interactions, may miss
predictions or hypothetical interactions.
|
Wiki pages |
Github Page |
https://thebiogrid.org/
|
Many Organisms |
|
No |
| Intact |
Molecular Interaction |
Database of molecular interactions, focusing
on protein-protein interactions (PPIs), including both experimentally
determined and predicted interactions.
|
Protein / Gene IDs |
Web output /
downloadable results
|
Web |
Creative
Commons Attribution 4.0 International (CC BY 4.0)
License and Apache License, Version 2.0
|
Browser |
Browser |
IntAct provides a
free, open source database system and analysis
tools for molecular interaction data. All interactions are derived from
literature curation or direct user submissions.
|
Robust data integration, supports many
organisms, extensive molecular interaction data.
|
Primarily focused on molecular interactions,
not all interactions are experimentally verified.
|
Detailed user guide |
No specific community forum |
https://www.ebi.ac.uk/intact/home
|
Many Organisms |
|
No |
| Complex Portal |
Macromolecular Complexes |
Provides detailed information on the
composition and interactions of protein complexes.
|
Protein / Gene IDs |
Web output /
downloadable results
|
Web |
Creative Commons Public Domain (CC0) License and Apache License, Version 2.0
|
Browser |
Browser |
The Complex Portal is
an encyclopaedic resource of macromolecular
complexes from a number of key model organisms. In addition to the expert
manually curated complexes, the portal now holds high-confidence
machine-learning predicted human complexes from hu.MAP3.0 and MuSIC. All data
is freely available for search and download.
|
Focus on protein complexes, integrates data
from multiple sources.
|
Primarily human-centric, may not cover all
types of protein complexes.
|
Detailed user guide |
No specific community forum |
https://www.ebi.ac.uk/complexportal/home
|
Human |
|
No |
| Human Protein
Atlas
|
Expression database |
Provides information on the expression
profiles of proteins in human tissues, organs, and cell lines.
|
Protein / Gene IDs |
Web output /
downloadable results
|
Web |
Creative Commons Attribution-ShareAlike 4.0 International License |
Browser |
Browser |
The Human Protein Atlas is a Swedish-based program initiated in 2003 with
the aim to map all the human proteins in cells, tissues, and organs using an
integration of various omics technologies, including antibody-based imaging,
mass spectrometry-based proteomics, transcriptomics, and systems biology. All
the data in the knowledge resource is open access to allow scientists both in
academia and industry to freely access the data for exploration of the human
proteome.
|
Rich tissue expression data, visualization
tools for protein localization.
|
Focused mainly on human tissues, limited for
non-human species.
|
About page |
No specific community forum |
https://www.proteinatlas.org/
|
Human |
|
No |
| Allen Brain
Map
|
Expression database |
Provides data on gene expression and brain
activity in human and other species’ brains, with spatial resolution.
|
Cell / Tissue types / Gene IDs |
Web output /
downloadable results
|
Web |
Open (See:
Terms of Use
|
Browser |
Browser |
The Allen Brain Atlas
is a free, online resource that maps gene
expression, connectivity, and neuroanatomical information for the brains of
mice, humans, and non-human primates. Data modalities such as gene expression
and neural connectivity are deposited to the atlas by researchers. All data
is availble for download both as raw as well as processed and annotated data
|
Excellent resource for neurobiology research,
detailed brain maps.
|
|
Tutorial videos available |
No specific community forum |
https://portal.brain-map.org/
|
Human and Mouse |
|
No |
| Ensembl |
Genome database |
Provides genome-wide annotations, variants,
gene expression data, and regulatory information across many species.
|
Gene ID / name / Coordinates / Variant information |
Web output /
downloadable results
|
Web |
Apache 2.0 software license |
Browser |
Browser |
Ensembl is a genome browser for vertebrate genomes that supports research in
comparative genomics, evolution, sequence variation and transcriptional
regulation. Ensembl annotate genes, computes multiple alignments, predicts
regulatory function and collects disease data. Ensembl tools include BLAST,
BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported
species.
|
Highly versatile, covers many species,
integration with genome browsers.
|
The vast amount of data can be overwhelming,
may require significant computing power for large-scale analyses.
|
Detailed documentation page / wiki |
No specific community forum |
https://useast.ensembl.org/index.html
|
Many Organisms |
|
Yes |
| Human Cell
Atlas
|
Expression database |
Maps the gene expression profiles of human
cells, providing high-resolution data on cell types and states.
|
Gene IDs / Tissue types |
Web output /
downloadable results
|
Web |
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0
International License.
|
Browser |
Browser |
The Human Cell Atlas is a global consortium that is mapping every cell type
in the human body, creating a 3-dimensional Atlas of human cells to transform
our understanding of biology and disease. The Atlas is likely to lead to
major advances in the way illnesses are diagnosed and treated. Data is avable
from many different tissues, labs and donors all freely
|
Highly detailed and resolution-specific, major
resource for cell biology.
|
Focused primarily on human cells, may require
advanced computational tools for analysis.
|
Detailed guides |
Slack and Github |
https://www.humancellatlas.org/
|
Human |
|
No |
| Genomics Data
Commons
|
Genomics, Cancer Data |
Provides genomic, transcriptomic, and clinical
data primarily for cancer research, integrated from large-scale cancer genome
studies.
|
No input |
Web output /
downloadable results
|
Web |
See: https://gdc.cancer.gov/about-gdc/gdc-policies |
Browser |
Browser |
The NCI’s Genomic Data Commons (GDC) provides the cancer research community
with a repository and computational platform for cancer researchers who need
to understand cancer, its clinical progression, and response to therapy. The
GDC supports several cancer genome programs at the NCI Office of Cancer
Genomics (OCG), including The Cancer Genome Atlas (TCGA) and Therapeutically
Applicable Research to Generate Effective Treatments (TARGET). Data from more
than 40000 cases are available for download.
|
Large dataset, highly relevant for cancer
research.
|
Focused primarily on cancer genomics; may not
be as broadly applicable to non-cancer research.
|
Detailed About the data section |
No specific community forum |
https://gdc.cancer.gov/
|
Human |
|
Yes |
| Pediatric
Cancer Platform
|
Genome database |
Provides genomic and clinical data for
pediatric cancer research, including patient data, somatic mutations, and
expression profiles.
|
Gene ID / Tissue Type / Study Type |
Web output /
downloadable results
|
Web |
Open (See: https://www.stjude.org/legal.html) |
Browser |
Browser |
The PeCan platform presents curated pediatric cancer genomics data including
variants, mutational signatures, and gene expression data in addition to
histological slide images* from ~9000 hematological, CNS, and non-CNS solid
tumor patient samples. Data can be explored via a series of data facets
containing both retrospective and prospective study cohorts from St. Jude
Children’s Research Hospital and other trusted institutions and research
centers around the world.
|
Highly valuable for pediatric cancer research, provides extensive patient data. |
Niche focus on pediatric cancers, limited
scope for non-cancer data.
|
Documentation on data output types |
No specific community forum |
https://pecan.stjude.cloud/
|
Human |
|
No |
| MaveDB |
Protein Function, Evolutionary Analysis |
Database of multiplexed assay of variant
effects (MAVEs), analyzing how genetic variants affect protein function.
|
Gene ID / Protein ID / Coordinates / Variant information |
Web output /
downloadable results
|
Web |
MaveDB is open-source, released under the AGPLv3 license. |
Browser |
Browser |
MaveDB is a public repository for datasets from Multiplexed Assays of
Variant Effect (MAVEs), such as those generated by deep mutational scanning
(DMS) or massively parallel reporter assay (MPRA) experiments.
|
Focuses on evolutionary analysis of protein
function.
|
Primarily for protein variants, may not be
suitable for large-scale genome-wide studies.
|
Documentation page for tutorials |
No specific community forum |
https://www.mavedb.org/
|
Human |
|
No |
