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View article: MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Open
We present the latest version of the Molecular Evolutionary Genetics Analysis (M ega ) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, M ega has been optimized for u…
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms Open
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and L…
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STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Open
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein …
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Minimap2: pairwise alignment for nucleotide sequences Open
Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or in…
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Metascape provides a biologist-oriented resource for the analysis of systems-level datasets Open
A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of curr…
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era Open
IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded …
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SWISS-MODEL: homology modelling of protein structures and complexes Open
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and serve…
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clusterProfiler 4.0: A universal enrichment tool for interpreting omics data Open
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible. To meet these requirements…
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update Open
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of …
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Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation Open
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tre…
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GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses Open
Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. While certain existing web servers are v…
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Accurate structure prediction of biomolecular interactions with AlphaFold 3 Open
The introduction of AlphaFold 2 1 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design 2–6 . Here we describe our AlphaFold 3 model wi…
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Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Open
The outbreak of a novel coronavirus (2019-nCoV) represents a pandemic threat that has been declared a public health emergency of international concern. The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, an…
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The mutational constraint spectrum quantified from variation in 141,456 humans Open
Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in na…
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The biology <b>,</b> function <b>,</b> and biomedical applications of exosomes Open
Clinical uses of cellular communication Exosomes are a type of extracellular vesicle that contain constituents (protein, DNA, and RNA) of the cells that secrete them. They are taken up by distant cells, where they can affect cell function …
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KEGG: new perspectives on genomes, pathways, diseases and drugs Open
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database proj…
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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets Open
Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are particularly important due to their versatility, specificity and adaptability. The STRING da…
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UniProt: a worldwide hub of protein knowledge Open
The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a mil…
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads Open
The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long re…
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The MR-Base platform supports systematic causal inference across the human phenome Open
Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, …
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Canu: scalable and accurate long-read assembly via adaptive <i>k</i> -mer weighting and repeat separation Open
Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accur…
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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Open
The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unpre…
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Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies Open
The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the curren…
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The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible Open
A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted pro…
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Inference and analysis of cell-cell communication using CellChat Open
Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their c…
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Pfam: The protein families database in 2021 Open
The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been …
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The PRIDE database and related tools and resources in 2019: improving support for quantification data Open
This FAIRsharing record describes: The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identificat…
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DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets Open
We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel function…
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The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest Open
Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scat…
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International System for Human Cytogenetic Nomenclature Open
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