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KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking genomes to life and the environment

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PHYRE2 Protein Fold Recognition Server

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The PHYRE automatic fold recognition server for predicting the structure and/or function of your protein sequence.

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https://www.ncbi.nlm.nih.gov/omim

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https://www.fruitfly.org/seq_tools/splice.html

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BDGP: Splice Site Prediction by Neural Network

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http://biosig.unimelb.edu.au/dynamut2/

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Carlos H.M. Rodrigues, Douglas E.V. Pires & David B. Ascher description

Abstract: Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon static structures. Here we present DynaMut, a web server implementing two distinct, well established normal mode approaches, which can be used to analyse and visualise protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes. DynaMut integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability. We demonstrate our approach outperforms alternative approaches to predict the effects of mutations on protein stability and flexibility (p-value < 0.001), achieving a correlation of up to 0.70 on blind tests. DynaMut also provides a comprehensive suite for protein motion and flexibility analysis and visualisation via a freely available, user friendly web server.

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Carlos H.M. Rodrigues, Douglas E.V. Pires & David B. Ascher description Abstract: Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon static structures.

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https://www.ebi.ac.uk/pdbe/

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Have you ever wondered what spider webs are made of, and why they are so strong and sticky? The protein which inspired the artwork for our featured structure for March 2021 is fibroin, an insoluble protein present in the silk produced by numerous insects. This article is guaranteed spider-picture-free.

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https://mole.upol.cz/

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MOLEonline web interface provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.

MOLE 2.5 is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies.

MOLEonline features

Quickest channel calculation on the market

Automatic transmembrane pore identification

Layered channel profile - geometry, length and radius

List of residues lining channels (distinguishing sidechain/mainchain contact with the channel)

Layered or channel-wise physico-chemical properties (several types of channel radius, length, charge, polarity, hydropathy, hydrophobicity, mutability, etc.)

Interactive selection of start or end points via XYZ coordinates, residues, or surface tetrahedron or via PatternQuery language

Automatic active site identification using CSA for enzymes, cofactors, and cavity interiors (origins)

Interactive visualization of structure and channels with LiteMol

Optimization and visualization of start and end points

Cavity and molecular surface visualization

Download results - complete results as ZIP or PDF report, channel PDB files and scripts for PyMol, Chimera, or VMD visualization, rich JSON, and channel profile image as SVG or PNG

Two-ways connectivity with ChannelsDB (comparison and annotation)

Free of charge

Quick start

News

Attention

Update to Chrome 75 disables WebGL functionalities important for MOLEonline LiteMol visualization. We are working on fix on this issue. Meanwhile use other browsers for accessing MOLEonline.

Server room maintenance

We would like to announce that MOLEonline will not be available on Monday (December 17th) due to web server room maintenance. Sorry for the inconvenience.

New features and updates

New features in MOLEonline:

new Help button will allow to send us your troubled session so we can help you more thoroughly,

multiple layers can be selected/deselected to show average properties and list of residues only around important area of the channel.

New features in MOLEonline

New properties

Lipophilicity (logP and logD-like scales)

Water solubility (logS)

Pore mode improvements

Better CSV export

Residue annotation via API from Uniprot

Differences between individual versions of MOLEonline are listed at: http://mole.upol.cz/faq
ChannelsDB was published

The ChannelsDB database contains information about channel positions, geometry and physicochemical properties of reviewed and annotated channels from PDB database. It was published in Database issue of Nucleic Acids Research. You can reach ChannelsDB data available for queried PDB structure in Submission tab in right lower corner of MOLEonline GUI window.

New plugins for Pymol and Chimera

MOLEonline is supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047)

Sponsored by ELIXIR-CZ, UPOL, MUNI

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MOLEonline web interface provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis. MOLE 2.5 is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies.

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PrePPI: structure-based prediction of protein-protein interactions

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PrePPI is a database of predicted and experimentally determined protein-protein interactions (PPI) for the human proteome. Predicted interactions in the database are determined using a Bayesian framework that combines structural, functional, evolutionary and expression information. Currently, PrePPI contains 1.35 million PPIs for ~85% of the human proteome. The PrePPI database also contains experimentally determined interactions compiled from a set of publicly available databases that curate interactions from the literature, e.g., DIP, IntAct, HPRD, etc. Please refer to " Structure-based prediction of protein-protein interactions on a genome-wide scale (Nature 490, 556-560)", " A computational interactome and functional annotation for the human proteome (Elife. 5:e18715)", and " PrePPI: a structure-informed database of protein-protein interactions (NAR 41, D828-33)" for details of the prediction method and the database.

To query PrePPI for PPIs involving a protein, enter its UniProt accession number (e.g. P03989) or the common name (e.g. PRNP) of the gene or protein. Use "P1:P2" or "P1<=>P2" (e.g. PPARg:PAX) to search for a specific PPI. Consult the Help page for detailed instructions on using PrePPI and interpreting the results.

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PrePPI is a database of predicted and experimentally determined protein-protein interactions (PPI) for the human proteome. Predicted interactions in the database are determined using a Bayesian framework that combines structural, functional, evolutionary and expression information. Currently, PrePPI contains 1.35 million PPIs for ~85% of the human proteome.

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Single domain pair - DISPOT

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Source code and instructions for using standalone version including Docker image can be found here.

The complexity of protein-protein interactions ( PPIs) is further compounded by the fact that an average protein consists of two or more domains, structurally and evolutionary independent subunits. Experimental studies have demonstrated that an interaction between a pair of proteins is not carried out by all domains constituting each protein, but rather by a select subset. However, finding which domains from each protein mediate the corresponding PPI is a challenging task.

Domain Interaction Statistical POTential ( DISPOT), a simple knowledge-based statistical potential that estimates the propensity of an interaction between a pair of protein domains, given their superfamily level of the SCOPe domain classification. The statistical potential is derived based on the analysis of more than 352,000 structurally resolved protein-protein interactions obtained from DOMMINO, a comprehensive database on structurally resolved macromolecular interactions.

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Source code and instructions for using standalone version including Docker image can be found here. The complexity of protein-protein interactions ( PPIs) is further compounded by the fact that an average protein consists of two or more domains, structurally and evolutionary independent subunits.

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http://www.interactome-atlas.org/

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We are excited to share our study published in Journal of Molecular Biology. This study contributes to a deeper understanding of the cellular functions of UBE3A and its potential role in pathways that may be affected in Angelman syndrome, UBE3A-associated autism spectrum disorders, and human papillomavirus-associated cancers by integrating UBE3A-specific interaction measurements with proteome-scale binary and co-complex interactome data.

https://www.ncbi.nlm.nih.gov/pubmed/?term=29426014

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We are excited to share our study published in Journal of Molecular Biology. This study contributes to a deeper understanding of the cellular functions of UBE3A and its potential role in pathways that may be affected in Angelman syndrome, UBE3A-associated autism spectrum disorders, and human papillomavirus-associated cancers by integrating UBE3A-specific interaction measurements with proteome-scale binary and co-complex interactome data.

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Your access to the NCBI website at www.ncbi.nlm.nih.gov has been temporarily blocked due to a possible misuse/abuse situation involving your site. This is not an indication of a security issue such as a virus or attack. It could be something as simple as a run away script or learning how to better use E-utilities, http://www.ncbi.nlm.nih.gov/books/NBK25497/, for more efficient work such that your work does not impact the ability of other researchers to also use our site. To restore access and understand how to better interact with our site to avoid this in the future, please have your system administrator contact info@ncbi.nlm.nih.gov.

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Your access to the NCBI website at www.ncbi.nlm.nih.gov has been temporarily blocked due to a possible misuse/abuse situation involving your site. This is not an indication of a security issue such as a virus or attack.

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JavaScript required

Unfortunately, you cannot create a word cloud unless you enable JavaScript.

To find some recommended software (a web browser), see our community section on Problems.

A word cloud is an image made of words that together resemble a cloudy shape.
The size of a word shows how important it is e.g. how often it appears in a text - its frequency.

People typically use word clouds to easily produce a summary of large documents (reports, speeches), to create art on a topic (gifts, displays) or to visualise data (tables, surveys).

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Easy to make custom word art. Thousands enjoy every day. Fast & secure. WordItOut, the free word cloud generator online since 2010.

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The defense mechanism of our adaptive immune system relies on the antigen-recognition abilities of two molecules: T cell receptors (TCRs), attached to the surface of T cells, and immunoglobins (Igs), anchored to and secreted by B cells.

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The defense mechanism of our adaptive immune system relies on the antigen-recognition abilities of two molecules: T cell receptors (TCRs), attached to the surface of T cells, and immunoglobins (Igs), anchored to and secreted by B cells.

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Molecular Ancestry NETwork

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Molecular Ancestry Network

Network biology characterizes and describes quantitatively the networks of molecular interactions that operate in biological systems.
There is considerable interest in the processes underlying evolution of networks, especially evolution of metabolism. Cellular metabolism represents a collection of enzyme reactions and transport processes that convert metabolites into molecules capable of supporting cellular life. Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolic networks, using information derived from structural genomics. more...

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Molecular Ancestry Network, University of Illinois

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Network biology characterizes and describes quantitatively the networks of molecular interactions that operate in biological systems. There is considerable interest in the processes underlying evolution of networks, especially evolution of metabolism. Cellular metabolism represents a collection of enzyme reactions and transport processes that convert metabolites into molecules capable of supporting cellular life.

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Listi yfir gagnabanka og forrit

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Pathguide: The Pathway Resource List, provided by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC) aims to provide a comprehensive catalog of biological pathway resources available on the internet. Pathguide is a spin-off project of the BioPAX effort (http://www.biopax.org).

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Some useful examples to help you get started

Germline Variants

rs746753722 or CLN6 E227K or NM_017882.3(CLN6):c.679G>A or 15:68500735:C:T

TP53:R175L or NM_000546:R175L or NM_000546(TP53):p.Arg175Leu or TP53:c.524G>T or chr17-7578406-C-A or rs28934578

rs113488022, rs376932266

BRAF:c.1799T>G, FTO:c.46-43098T>C,

SYNGR1:c.607_608insACA,
BAIAP2L2:c.1322_1363del

15-73027478-T-C, X 153418497 A G

Deletions

chr2-131129929-GACGGG-, chr13-38320595-AA-, 5:156479558:15:

Insertions

chr22:39777823::CAA, 7-151945072--T

chr17:37800000:L100000:DUP, chr11:21200000:L90000:DEL, chr7:117138367:117159446:DEL,

chr3:37039445:37059613:DUP, chr21:36160098:36171759:DEL, chr1:110230496:110235917:DUP,

chr21:36160098:36171759:DEL, chr17:43098764:43110978:DEL, chr13:32317656:32331987:DUP,

chr8:127734450:127764981:DUP, chr1:13308329:13308887:DEL

More examples
Source Databases

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Mastermind - Comprehensive Genomic Search Engine

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Genomic evidence for diseases, genes and variants from the medical literature

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Genatjáning og Útraðir

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The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES and RNA-seq. Remaining samples are stored in the GTEx Biobank.

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NCBI Genome List

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Genome Aggregation Database - Stökkbreytingar

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The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.

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BLAST: Basic Local Alignment Search Tool

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The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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Multiple alignment program for amino acid or nucleotide sequences

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To avoid overload, try a light-weight option, for MSA of full-length SARS-CoV-2 genomes (2020/Apr).

The Q-INS-i option (for RNA) did not work because of a bug in version 7.489, Oct.23. Fixed in version 7.490, Oct.30, 2021.

A compatibility problem of MSAViewer with Chrome 92 and Firefox 90 has been fixed, Aug. 5, 2021.

For a large number of short sequences, try an experimental service.

Experimental service for aligning raw reads (2019/Aug)

Multiple sequence alignment and NJ / UPGMA phylogeny

Advanced settings

Parameters:

Scoring matrix for amino acid sequences:

Scoring matrix for nucleotide sequences:

↑ Switch it to '1PAM / κ=2' when aligning closely related DNA sequences.

Gap opening penalty: (1.0 - 5.0)

Offset value: (0.0 - 1.0)

↓ Long stretches of Ns tend to be gapped (excluded from the alignment).

↑ Try this if Ns should be aligned with usual letters.

References

Katoh, Rozewicki, Yamada 2019 (Briefings in Bioinformatics 20:1160-1166)
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kuraku, Zmasek, Nishimura, Katoh 2013 (Nucleic Acids Research 41:W22-W28)
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

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MAFFT alignment and NJ / UPGMA phylogeny

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To avoid overload, try a light-weight option, for MSA of full-length SARS-CoV-2 genomes (2020/Apr). The Q-INS-i option (for RNA) did not work because of a bug in version 7.489, Oct.23. Fixed in version 7.490, Oct.30, 2021. A compatibility problem of MSAViewer with Chrome 92 and Firefox 90 has been fixed, Aug.

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LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or nucleotide sequences.

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LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or DNA sequences

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Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments

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Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools.

Important note: This tool can align up to 4000 sequences or a maximum file size of 4 MB.

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Clustal Omega is a multiple sequence alignment program. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

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Curated, non-redundant set of transcription factor binding sites for eukaryotes.

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The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.

When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount

Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, and Mathelier A JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles Nucleic Acids Res. journal_details; doi: NA

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JASPAR - A database of transcription factor binding profiles

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The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality. When should it be used?

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Intergovernmental organisation that brings together life science resources from across Europe.

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A distributed infrastructure for life-science information

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AlphaFold Protein Structure Database

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AlphaFold colab

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Workbench for protein structure analysis.

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UCL Computer Science Department Bioinformatics Group

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Evaluates a wide variety of protein sequence properties using statistics

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Statistical Analysis of Protein Sequences

SAPS evaluates a wide variety of protein sequence properties using statistics. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types.

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Statistical Analysis of Protein Sequences.

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Your query returned no results.

Service currently not available for [[service_error_message]]

Orthologs predicted by OMA and OrthoDB for [[term]] at taxonomic level "[[ selected_level ]]"

SwissOrthology provides a unified entry point to orthology resources from SIB.

Under the SwissOrthology umbrella the SIB provides a variety of resources centered around orthology. Orthologs are genes that have started diverging through a speciation event. As they have been by definition the same gene until speciation, orthologs play an important role in many bioinformatics applications such as gene function prediction, species tree reconstruction or comparative analyses.

SwissOrthology is a collaboration between the two research labs run by Christophe Dessimoz at University Lausanne and Evgeny Zdobnov at University of Geneva. The two labs develop and maintain two of the world leading resources for orthology: and OrthoDB.

Find out more about the collaboration.

Interactive Guide how to choose Orthology Resource

In the interactive guide we try to help you to find the right orthology resource for your application.

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Your query returned no results. [[uniprot_protein_info.fullname]] Taxonomic Levels of HOGs for [[level_query_result.query_id]] Service currently not available for [[service_error_message]] Orthologs predicted by OMA and OrthoDB for [[term]] at taxonomic level "[[ selected_level ]]" SwissOrthology provides a unified entry point to orthology resources from SIB. Under the SwissOrthology umbrella the SIB provides a variety of resources centered around orthology.

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Search Multispecies Groups Search Specific Groups Please select one or more species from the species lists (on the left). To select non-contiguous species, press and hold the "Ctrl" key on your keyboard.

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STRING: functional protein association networks

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DIOPT - DRSC Integrative Ortholog Prediction Tool

New

Version 8
+ Updated Ortholog sources
Previous Version 7
+ Add Arabidopsis thaliana
+ Add 3 prediction algorithms (Hieranoid, OrthoFinder, OrthoInspector)
+ Allow user to submit missing relationships
+ Allow user to add feedback

Version 8.0 (Aug 2019)
Details of this tool are published in Hu, et. al.

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DRSC - DRSC Integrative Ortholog Prediction Tool

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DIOPT - DRSC Integrative Ortholog Prediction Tool Version 8 + Updated Ortholog sources Previous Version 7 + Add Arabidopsis thaliana + Add 3 prediction algorithms (Hieranoid, OrthoFinder, OrthoInspector) + Allow user to submit missing relationships + Allow user to add feedback Version 8.0 (Aug 2019) Details of this tool are published in Hu, et.

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OMA is a method and database for the inference of orthologs among complete genomes. We provide browsable orthology predictions, APIs, flat file downloads and a standalone version of the inference algorithm.

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Links unique leaf labels to lists of variables/values pairs of annotations, independently of the tree topologies, remaining fully compatible with the basic newick format.

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GEMI Bioinformatics F. Chevenet
U.M.R. 2724 CNRS-IRD & U.R. 165 IRD Génétique et Evolution des Maladies Infectieuses
Centre de Recherche I.R.D. 911, Avenue Agropolis - BP 64501 34394 Montpellier Cedex 5 - France

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phylogeny ; tree editor ; editor ; annotations ; dynamic graphics ; information visualization

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GEMI Bioinformatics F. Chevenet U.M.R. 2724 CNRS-IRD & U.R. 165 IRD Génétique et Evolution des Maladies Infectieuses Centre de Recherche I.R.D. 911, Avenue Agropolis - BP 64501 34394 Montpellier Cedex 5 - France

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Visualize support values. Explore clade distances.

Branch support values and other metadata can be visualized as various shapes with adjustable colors and sizes or as text labels. Alternatively, branch colors or widths can be linked to the underlying data values.

Trees with branch length information can have an internal scale with adjustable levels and colors, allowing easy estimation of distances between various clades.

Upload a tree Create an account

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Branch support values and other metadata can be visualized as various shapes with adjustable colors and sizes or as text labels. Alternatively, branch colors or widths can be linked to the underlying data values. Trees with branch length information can have an internal scale with adjustable levels and colors, allowing easy estimation of distances between various clades.

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TimeTree of Life

TimeTree is a public knowledge-base for information on the evolutionary timescale of life. Data from thousands of published studies are assembled into a searchable tree of life scaled to time. Three search modes are possible:

- to find the divergence time of two species or higher taxa

- to drill back through time and find evolutionary branches from the perspective of a single species

- to build a timetree of a group of species or custom list

showing events in geological time and astronomical history are provided for comparison with timelines and timetrees. Results can be exported in different formats for additional analyses and publication.

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TimeTree is a public knowledge-base for information on the evolutionary timescale of life. Data from thousands of published studies are assembled into a searchable tree of life scaled to time.

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A Structural View of Biology.

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As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are…

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Draws a hydropathy plot for your protein sequence.

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Plot amino acid properties of a protein sequence

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High-quality protein structure prediction.

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FREE FOR ACADEMIC RESEARCH

HIGH-QUALITY

FALCON2 can predict high-quality protein structures with average TMscore above 0.7, even for CASP domain targets.

FAST

FALCON2 can directly predict the three-dimensional conformation of the protein from the amino acid sequence in a few hours.

EASY-TO-USE

FALCON2 shows not only the final output structure, but also some intermediate outputs, including the predicted inter-residue distance matrix and the selected template. The predicted structures are intuitively visualized using 3Dmol.

Accurate remote homologue identificaiton

High-quality structure prediction

Suitful to proteome-wide structure prediction

More on FALCON2

FALCON2 incorporates two prediction approaches: a TBM prediction approach ProALIGN, and an prediction approach ProFOLD, to obtain higher quality of protein structure prediction.

FALCON2 employs ProALIGN to exploit structure information of homologous templates of target proteins.

FALCON2 employs ProFOLD to exploit the co-evolutionary information carried by homologous proteins.

By more friendly interface and higher prediction performance, We hope FALCON2 enables protein structure prediction even in the non-expert laboratory and can contribute to a better understanding of protein structures and functions in the health and disease.

We predicted structures for a total of 6033 mouse proteins in 6 days

We observed a significant correlation between protein half-lives and protein structural factors

FALCON was ranked the 3rd in the free modeling hard category in CASP8

FALCON@home-based prediction was ranked the 9th in the template-based modeling category in CASP11

OVER 20,000 VOLUNTEER CPUS

Running FALCON on CAS@home platform has achieved 1.27TFLOPS!

Over 20,000 volunteer CPUs are contributing computating power to FALCON@home

‹›

Contact Us

Bioinformatics Lab, Institute of Computing Technology
Chinese Academy of Sciences

6, Kexueyuan South Road, Zhongguancun
Beijing, China

(86)10-62600844

FALCON@ict.ac.cn

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FALCON2 - high-quality protein structure prediction

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FREE FOR ACADEMIC RESEARCH HIGH-QUALITY FALCON2 can predict high-quality protein structures with average TMscore above 0.7, even for CASP domain targets. FAST FALCON2 can directly predict the three-dimensional conformation of the protein from the amino acid sequence in a few hours.

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A helical wheel diagram for a protein sequence.

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Reverse and/or complement DNA sequences

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Reverse and/or complement DNA sequences. Separate sequences with line returns. Complementarity will follow theIUPAC convention.
IUPAC Degeneracies

Source: http://hornet.bio.uci.edu/~hjm/projects/tacg/ (no longer online)
* Thanks to Joost Kolkman at Maxygen who pointed out that revcomp(S)=S and revcomp(W)=W; in the source above (no longer online), revcomp(S) was W and vice-versa, which is is incorrect. I knew that but hadn't verified.

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Reverse and/or complement DNA sequences. Separate sequences with line returns. Complementarity will follow theIUPAC convention. IUPAC Degeneracies Source: http://hornet.bio.uci.edu/~hjm/projects/tacg/ (no longer online)* Thanks to Joost Kolkman at Maxygen who pointed out that revcomp(S)=S and revcomp(W)=W; in the source above (no longer online), revcomp(S) was W and vice-versa, which is is incorrect.

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A public web server for graph-based analysis of biological networks.

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[?] From direct input

[?] From a file in your computer

[?] From a file in our server

You can also use Advanced input to combine several datasets or to use other input formats.

Organism:

[?] Merge different IDs of same gene

[?] Convert orthologs

[?] Connected components
[?] Strongly connected components
[?] Biconnected components
[?] Whole graph
[?] Hub-based modules
[?] Maximal cliques
[?] MCL clustering
[?] Betweenness centrality clustering

[?] Network neighbourhood

Edge settings
[?] Remove edges with less than labels
[?] Keep % of heaviest edges
[?] Assign more weight to smaller networks
[?] Create global network (remove all labels)

Node settings
[?] Remove genes:
unknown ambiguous
[?] Keep % of most connected nodes

Module settings
[?] Hide modules with less than nodes
[?] Show largest modules
[?] Calculate functional scores using g:Profiler
[?] Sort modules by functional score
[?] Hide insignificant modules

Create a private data folder and upload files. These will appear in your input menu in the main window.

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GraphWeb: analysis of biological networks

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From direct input [?] From a file in your computer [?] From a file in our server You can also use Advanced input to combine several datasets or to use other input formats. Organism: [?] Merge different IDs of same gene [?] Convert orthologs [?] Connected components [?] Strongly connected components [?]

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Bioinformatics resource portal of the SIB.

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SIB Swiss Institute of Bioinformatics | Expasy

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Operated by the SIB Swiss Institute of Bioinformatics, Expasy, the Swiss Bioinformatics Resource Portal, provides access to scientific databases and software tools in different areas of life sciences.

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Color Schemes and Palettes

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Color Combinations

The Combo Library contains pages of color combinations (a.k.a, color schemes and color palettes) for you to choose from. Each color scheme contains the html color codes you will need when coding your website template. The hex codes can be found underneath each of the color swatches.

Click on a color combinations name to test it out. This link will take you to the Combo Tester, where you can view a larger version of each color palette.

The Combo Library provides a convenient way to search color schemes. If you are looking for colour schemes with particular color codes, simply enter those html colors into the search box. For example, entering #FFFFFF will narrow down the list to only combinations containing the color white.

You can click on individual hex color codes to view them full screen through the Combo Tester. On the Combo Tester page you can use the 'Get the Image' dropdown option in order to grab the color swatch.

# data[].attributes.attachment_link.description
The Combo Library contains pages of color combinations (a.k.a, color schemes and color palettes) for you to choose from. Each color scheme contains the html color codes you will need when coding your website template. The hex codes can be found underneath each of the color swatches.

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Amino acid indices, substitution matrices and pair-wise contact potentials.

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AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature.

Search or Download

(e.g. Hydrophobicity, MIRL960101)

Figures and Lists

References

Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988). [PMID:3244698]

Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). [PMID:9053899]

Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 27, 368-369 (1999). [PMID:9847231]

Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000). [PMID:10592278]

Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M.; AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-D205 (2008). [PMID:17998252]

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AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials.

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Generates phylogenetic trees based on the NCBI taxonomy or Genome Taxonomy Database.

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phyloT generates phylogenetic trees based on the NCBI taxonomy or Genome Taxonomy Database. From a list of taxonomic names, identifiers or protein accessions, phyloT will generate a pruned tree in the selected output format. Complete clades can be simply included, with interruption at desired taxonomic levels and with optional filtering of unwanted nodes. Please check the help page for detailed information.

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phyloT generates phylogenetic trees based on the NCBI taxonomy or Genome Taxonomy Database. From a list of taxonomic names, identifiers or protein accessions, phyloT will generate a pruned tree in the selected output format. Complete clades can be simply included, with interruption at desired taxonomic levels and with optional filtering of unwanted nodes.

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SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.

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You can use SMART in two different modes: normal or genomic.The main difference is in the underlying protein database used. In Normal SMART, the database contains Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes. In Genomic SMART, only the proteomes of completely sequenced genomes are used; Ensembl for metazoans and Swiss-Prot for the rest. The complete list of genomes in Genomic SMART is available here.

The protein database in Normal SMART has significant redundancy, even though identical proteins are removed. If you use SMART to explore domain architectures, or want to find exact domain counts in various genomes, consider switching to Genomic mode. The numbers in the domain annotation pages will be more accurate, and there will not be many protein fragments corresponding to the same gene in the architecture query results. Remember you are exploring a limited set of genomes, though.

Different color schemes are used to easily identify the mode you're in.

Normal mode Genomic mode

Click on the images above to select your default mode.

Information about your selected mode is stored in a browser cookie. If you for whatever reason don't want/can't use cookies, access SMART through this page.

You can easily change modes later, by clicking on the links in the 'SMART MODE' header box, or in your personal preference settings ('SETUP' link in the menu):

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You can use SMART in two different modes: normal or genomic.The main difference is in the underlying protein database used. In Normal SMART, the database contains Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes. In Genomic SMART, only the proteomes of completely sequenced genomes are used; Ensembl for metazoans and Swiss-Prot for the rest.

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A comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

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If you are not seeing anything on this page, it might be for multiple reasons:

You might have JavaScript disabled: make sure to enable JavaScript on your browser, or use a browser that supports JavaScript.

You might have an outdated browser: make sure that your browser is up to date as older versions might not work with the website.

There might have been a network issue: ensure that your connectivity is stable and try to reload the page to see if it solves the issue. Reload this page

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Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties such as aromaticity, charge, polarity, hydrophobicity, flexibility, surface exposure, solvation potential, interface propensity, normalized frequency of occurrence in α helices, β structures, and coils, linker and disorder propensities, size and bulkiness.

Composition Profiler takes two samples of amino acid sequences as input, namely the query sample and the reference sample. The reference sample provides the background amino acid distribution. Suitable background distributions can be chosen according to the nature of the query sample, e.g., a standard amino acid datasets (such as SwissProt, PDB Select 25, DisProt, or surface residues of monomeric proteins), or a representative sample of proteins from the organism under study, or a group of proteins that have a contrasting functional annotation to the query sample.

The graphical output of our tool is a bar chart composed of twenty data points (one for each amino acid), where bar heights indicate enrichment or depletion. The output is designed to assist the discovery of statistically significant composition anomalies by color-coding and sorting residues according to their physico-chemical properties. For example, if the property being tested is flexibility, the tool will group rigid amino acids on the left hand side of the plot and flexible amino acids on the right hand side of the plot.

Acknowledgements

Composition Profiler software was developed by Vladimir Vacic and Stefano Lonardi (University of California, Riverside), and Vladimir N. Uversky and A. Keith Dunker (Indiana University School of Medicine, Indianapolis).

In citing this program, please refer to:

Vacic V., Uversky V.N., Dunker A.K., and Lonardi S. "Composition Profiler: A tool for discovery and visualization of amino acid composition differences". BMC Bioinformatics. 8:211. (2007)

Composition Profiler was created using the Ruby programming language. Routines for calculating p-values were written in C and use numerical approximation functions from the Stephen L. Moshier's Cephes Math Library.

Source Code

Composition Profiler source code is available for download. The README file contains installation instructions, and licensing information can be found in the LICENSE file.

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Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties such as aromaticity, charge, polarity, hydrophobicity, flexibility, surface exposure, solvation potential, interface propensity, normalized frequency of occurrence in α helices, β structures, and coils, linker and disorder propensities, size and bulkiness.

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Prediction of Order and Disorder by evaluation of NMR data

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Pepinfo creates a variety of plots that display different amino acid properties.

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Plot amino acid properties of a protein sequence

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Explores the component aspect of Protein Structure space.

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Contact String the Topology representation : Given a protein structure, ProLego enumerates constituent secondary structures and their arrangements. This is represented as a unique 1D string.

Generate topology visualization:

A 2D topology representation

A 1D or Linear topology representation

where secondary structures will be present as per their chain connectivity N to C and contact between SSEs will be assigned by different arcs connecting them.
Topology Classifier: Comparing the obtained "contact string" with studied datasets, ProLego assigns frequency of occurrence status (prevalent/non-prevalent) for the corresponding topology. If the topology is not available in the dataset it should be able to update database on the fly.

Module Analysis: Given a contact String ProLego server can extract all the possible modules and searches similar proteins in the database.

Contact Map: Plots secondary structure contact map given a protein structure

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Contact String the Topology representation : Given a protein structure, ProLego enumerates constituent secondary structures and their arrangements. This is represented as a unique 1D string. Generate topology visualization: A 2D topology representation A 1D or Linear topology representation where secondary structures will be present as per their chain connectivity N to C and contact between SSEs will be assigned by different arcs connecting them.

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Pictorial database of 3D structures in the Protein Data Bank

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PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank ( PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them.
Also included are the AlphaFold predicted models for all human protein for comparison with experimentally determined structures. Read more ...

Scans all TITLE, HEADER, COMPND, SOURCE and AUTHOR records in the PDB (eg to find a given protein by name).

Perform FASTA search vs all sequences in the PDB to get a list of the closest matches.

COVID-19 structures

The SARS-CoV-2 virus genome has 14 open reading frames coding for at least 29 protein: four structural proteins, making the outer coat and its characteristic protruding spikes, sixteen or more non-structural proteins involved in the virus's replication, and nine accessory proteins that are thought to counteract the host's immune response.

Many of the proteins have been structurally determined and deposited in the PDB. Three examples are shown below.

For the full list, go to COVID-19 protein structures

Spike protein. The spikes on the surface of the virus bind to specific host cell receptors and initiate cell infection. The structure shows a trimeric complex of the spike glycoprotein (in its closed state).
PDB entry 6vxx
Pubmed ref 32155444

Main protease responsible for cleaving the main polyprotein into its separate non-structural proteins, here shown with a bound inhibitor.
PDB entry 5r81

RNA-binding domain of the nucleocapsid phosphoprotein. Tetrameric complex of N-terminal domains of the protein which is a facilitator for reverse transcription and integration.
PDB entry 6vyo

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PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank ( PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them.

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Create helical wheel diagrams for coiled coils.

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DrawCoil 1.0

This program creates helical wheel diagrams for coiled coils of any oligomerization state and orientation. The program is provided as is. Contact gevorg.grigoryan at gmail dot com with bug reports and requests. Logo art by Sona Ayvazyan. Stand-alone script can be downloaded from here.

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DrawCoil 1.0 This program creates helical wheel diagrams for coiled coils of any oligomerization state and orientation. The program is provided as is. Contact gevorg.grigoryan at gmail dot com with bug reports and requests. Logo art by Sona Ayvazyan. Stand-alone script can be downloaded from here.

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An interactive exploration tool for investigating the functional and evolutionary features of proteins.

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Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey

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ProViz - protein interactive exploration tool

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ProViz is an interactive protein exploration tool, which searches several databases for information about a given query protein. Data relevant to the protein like an alignment of homologues, linear motifs, post translational modifications, domains, secondary structure, sequence variations and others are graphically represented relative to their position in the protein.

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A web server for functional enrichment analysis and conversions of gene lists.

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g:Profiler - a web server for functional enrichment analysis and conversions of gene lists

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A genome browser for vertebrate genomes.

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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.

Update to GENCODE 34 (human) and GENCODE M25 (mouse)

Update of gnomAD genomic allele frequencies to version 3

New genomes: 3 mammals, 7 fish, 6 birds, 4 reptiles

Updated genomes: Platypus and Northern Pike

New interface for configuration of multidimensional track hubs

More release news on our blog

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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.

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National Center for Biotechnology Information

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The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

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A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data.

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DOI: 10.18129/B9.bioc.trackViewer

A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Bioconductor version: Release (3.12)

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Author: Jianhong Ou [aut, cre] , Julie Lihua Zhu [aut]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Citation (from within R, enter citation("trackViewer")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("trackViewer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("trackViewer")

Details

Package Archives

Follow Installation instructions to use this package in your R session.

Source Repository

git clone https://git.bioconductor.org/packages/trackViewer

Source Repository (Developer Access)

git clone git@git.bioconductor.org:packages/trackViewer

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DOI: 10.18129/B9.bioc.trackViewer Bioconductor version: Release (3.12) Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

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Visual collaboration suite.

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Lucid visual collaboration suite: Log in

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Go from imagining the future to building it. Log in to access Lucidchart for intelligent diagramming or Lucidspark for virtual whiteboarding. Teams can collaborate, ideate, and build projects in real time.

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A web based application designed to make the generation of sequence logos as easy and painless as possible.

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References

Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,
Genome Research, 14:1188-1190, (2004) [ Full Text ]

Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100

Introduction

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Clickhere to create your own sequence logos.

Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

WebLogo Source Code

The WebLogo source code is available for download. See the README file for installation instructions and release notes, and LICENSE for the open source license.

Disclaimer

While no permanent records are kept of submitted sequences, we cannot undertake to guarantee that data sent to WebLogo remains secure. Moreover, no guarantees whatsoever are provided about data generated by WebLogo.

Acknowledgements

WebLogo was created by:

Gavin E. Crooks, Gary Hon, John-Marc Chandonia and Steven E. Brenner,
Computational Genomics Research Group,
Department of Plant and Microbial Biology,
University of California, Berkeley

WebLogo is based upon the programs alpro and makelogo, both of which are part of Tom Schneider's delila package. Many thanks are due to him for making this software freely available and for encouraging its use.

The Look & Feel of the sequence logo generation form was inspired by the GIF/PNG-Creator for 2D Plots of Chemical Structures.

Feedback

Suggestions on how to improve WebLogo are heartily welcomed! Please email logo@compbio.berkeley.edu

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Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [ Full Text ] Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100 WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

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Sequence logo generator

Seq2Logo is a web-based sequence logo generation method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.

Note that Seq2Logo as default includes a pseudo count correction for lowcounts. This means that the amino acid frequencies displayed in the sequence logos are corrected for low number of observations using a Blosum amino acid similarity matrix. To turn this feature off, the Weight on prior must be set to zero.

Submission Instructions Output format Abstract Downloads

GETTING HELP

Correspondence: Technical Support:

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Seq2Logo is a web-based sequence logo generation method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. Note that Seq2Logo as default includes a pseudo count correction for lowcounts.

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Helps you visualize and compare your gene lists from different experiments.

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DiVenn can help you visualize and compare your gene lists from different experiments. It currently accepts two-column tab-delimited expression data and user-defined custom data. The following new functions have been added in DiVenn2:

Show the number of common and unique genes between experimental comparisons in the DiVenn graph

Change the color and shape of nodes

Visualize custom data if species of interest are not supported in DiVenn

If you use this tool in your research, please use the following citation in your manuscript.

Sun, Liang*, Sufen Dong, Yinbing Ge, Jose P. Fonseca, Zachary Robinson, Kirankumar Mysore, Perdeep Mehta. "DiVenn: An Interactive and Integrated Web-based Visualization Tool for Comparing Gene Lists." Frontiers in Genetics 10 (2019):421.

Submit Data

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DiVenn can help you visualize and compare your gene lists from different experiments. It currently accepts two-column tab-delimited expression data and user-defined custom data.

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Hlutfallslegir hringir

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bioinformatics evolutionary genomics ghent calculate and draw online venn diagrams 6-way

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Online tool to create custom Venn/Euler diagrams up to 6 sets and intersections for up to 30 sets

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Interactive Venn Diagrams

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Please cite:
Heberle, H.; Meirelles, G. V.; da Silva, F. R.; Telles, G. P.; Minghim, R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16:169 (2015).

DOI: 10.1186/s12859-015-0611-3

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InteractiVenn - Interactive Venn Diagrams

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InteractiVenn is an interactive visualization tool for analyzing lists of elements using Venn diagrams. The web tool supports up to six different sets. Moreover, union operations between sets can be made. The union operations are reflected to the Venn diagram. Other interactions are also available, such as color changing and export diagram in SVG and PNG format.

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Up to six lists.

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Click on a venn diagram figure to display the linked elements:

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Area-Proportional Venn Diagrams Using Deep Learning

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DeepVenn - Create Area-Proportional Venn Diagrams Using Deep Learning

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Venn diagram generator. Please use it for the creation of area-proportional Venn diagrams for scientific publications and presentations. Give it a try!

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Free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.

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Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied.

By contrast, Pairwise Sequence Alignment tools are used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences.

MUSCLE

MView

Transform a Sequence Similarity Search result into a Multiple Sequence Alignment or reformat a Multiple Sequence Alignment using the MView program.

Launch MView

T-Coffee

WebPRANK

The EBI has a new phylogeny-aware multiple sequence alignment program which makes use of evolutionary information to help place insertions and deletions.
Try it out at WebPRANK.

The tools described on this page are provided using The EMBL-EBI search and sequence analysis tools APIs in 2019

Please read the provided Help & Documentation and FAQs before seeking help from our support staff. If you have any feedback or encountered any issues please let us know via EMBL-EBI Support. If you plan to use these services during a course please contact us. Read our Privacy Notice if you are concerned with your privacy and how we handle personal information.

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Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied. By contrast, Pairwise Sequence Alignment tools are used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences.

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A customizable Venn diagram for up to five lists and diplay a matrix of all pairwise intersections.

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Find the intersection of two lists.

Find the difference between two lists.

Compare two lists.

Find data overlap.

Compare more than 4 lists.

Online Venn diagram for up to four lists.

Online Jaccard index calculation.

Compare data sets to find their intersection.

Find which items are shared by two or more lists.

Multiple List Comparator is an alternative to Venny.

Multiple List Comparator is a Venn diagram drawing tool.

SETTINGS

The app can use a tabular dataset or individual data lists as the input. In the first case, click the "Tabular Input" heading and provide the data. In the latter case, the required number of empty list forms has to be prepared up front. This can be done by filling the number of lists to be prepared in the "Number of lists" field followed by clicking the "Set" button (all existing lists will be discarded). To add a list form to an existing set of forms, click the large plus button located just after the last list form.

To apply any changes made in the settings or in input data, click the "Compare" button.

LIST INPUT

The app expects an input in the form of simple item lists i.e. with one item per line. If the source data are to be loaded from files, the files should be plain text files (no formatting) containing one item per each line or comma-separated items.

TABULAR INPUT

The app can import a tabular dataset wherein the list items are organized column-wise and separated with delimiters in each row. The delimiter can be one of the characters tab, comma or semicolon and has to be properly chosen before reading the data into the app with the "Read Data" button. You can directly copy - paste data from Microsoft Excel or other spreadsheet programs. Choose tab as the delimiter in such cases. If the source data are to be loaded from a file, the file should be a plain text file containing delimiter-separated values. After clicking the "Read Data" button, the values should get properly distributed into individual input lists. If not, check the delimiter choice and appearance of the data. The problem may also be caused by a presence of additional text lines preceding the data. Such lines have to be removed manually.

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MULTIPLE LIST COMPARATOR - A free online tool to find list overlaps and draw Venn diagrams

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A free online tool to find data intersection and draw Venn diagrams. It accepts data as item lists or as a table with the input data in columns. It displays graphical and tabular results, and offers a variety of export options.

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Sorry, your screen size is too small to correctly display this page.

scatterplot.online allows you to make scatter plots easily.
Give it a try on your computer.
Read about it

copy paste here

csv data
excel table
url to csv

You have to copy-paste your data into the box above.

Save you current project. It will be only saved in your browser.

Your workspace is empty now.

Click SAVE button to save your current workspace.

It will be available even after you close the browser.

Right click (or hold control and click) on the image below and choose Save Image As...

PNG

It would mean a world to me if you could link to scatterplot.online or share it on social media 🙇

SVG

(｡*́︿*̀｡)
Is your data in correct format? Read upload tutorial.

Try with sample csv data below

Id, Value, Label
1, 2.4, on
2, 4.3, on
3, 6.6, off
4, 6.4, off

(｡*́︿*̀｡) Sorry, scatterplot.online is not supported by your browser.
Please try updating it.

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Sorry, your screen size is too small to correctly display this page. scatterplot.online allows you to make scatter plots easily.Give it a try on your computer. Read about it copy paste here csv dataexcel tableurl to csv You have to copy-paste your data into the box above. Save you current project.

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Biological pathway editor

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PathVisio is a free open-source pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. It is developed in Java and can be extended with plugins.

# data[].attributes.attachment_link.description
PathVisio is a free open-source pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. It is developed in Java and can be extended with plugins.