ERGO 2.0 provides a systems biology informatics toolkit centered on comparative genomics to capture, query, and visualize sequenced genomes.  Using Igenbio's proprietary algorithms, and the most comprehensive genomic database integrated with the largest collection of microbial metabolic and non-metabolic pathways, ERGO™ assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways, and gene products.  

ERGO 2.0’s hand-curated content combined with cutting edge genomics and bioinformatics tools help scientists in the biotechnology, agriculture, and pharmaceutical industries understand and design the underlying biology leading to new products faster.

ERGO Features

Featured
Metagenome/Microbiome Analysis
Metagenome/Microbiome Analysis

Easily analyze your metagenome projects using ERGO by dragging and dropping your BIOM file into ERGO. Compute the Principal Coordinates Analysis (PCoA), Richness Estimates, and Taxonomic Bar Charts at a click of a button. In addition, ERGO computes Analysis of Similarities (ANOSIM) to test the significance of group differences.

Learn more about Metagenome analysis in ERGO ▸

Introducing ERGO™ Workflows™
Introducing ERGO™ Workflows™

Simple, Fast, and Secure sequence analysis.

ERGO Workflows could not be easier - simply drag and drop your sequence files into ERGO and start your analyzing. There is no simpler way to perform RNA-Seq and Variant analysis.

Learn more about how ERGO Workflows can power your research needs.

Whole Genome Annotation Platform
Whole Genome Annotation Platform

ERGO is the premier annotation platform, providing scientists and researchers with deep insight into their strains. Using a combination of proprietary algorithms, sequence similarity, gene context clustering, regulatory and expression data ERGO can deduce the core functionality of prokaryotic and eukaryotic genomes.

Learn more about how we annotate genomes.

Genome Browser
Genome Browser

Visualize genomes by functional systems or subsystems and understand the distribution of metabolic and non-metabolic pathways. Powerful visualizations facilitate not only genome sequence comparison but also metabolic comparison for greater understanding of genome plasticity, gene displacement and orthologous displacements.

Learn more about ERGO 2.0's Genome Browser.

Differential Gene Expression Analysis
Differential Gene Expression Analysis

Integrate your expression data with ERGO to Identify differentially expressed genes from RNA-Seq, cDNA, EST, Microarray, and other expression studies. ERGO automatically performs statistical analysis presenting the differentially expressed genes in their metabolic context. Visualize your expression data on KEGG pathway maps. No knowledge of statistical techniques or tools are necessary.

Learn more about RNA-Seq and Expression Analytics in ERGO 2.0

Variant Detection and Analysis
Variant Detection and Analysis

Explore the variation between your strains. ERGO identifies and annotates Single Nucleotide Polymorphisms (SNPs), Insertions, and Deletions (InDels). Quickly discover ablated transcripts, frameshifts, start/stop codon loss, and more.

Read more about Variant detection, annotation, and analysis in ERGO.

Metabolic Analysis
Metabolic Analysis

ERGO 2.0 deduces the core metabolic functionality of a whole organism from genome sequence data. This enables scientists to accelerate their research for strain improvement, optimization, and product development.

Comparative Genomics
Comparative Genomics

ERGO 2.0 tools enable scientists to explore strain differences. Utilizing our publication proven Genome Align tool scientists are able to visually explore differences. Comparative protein clustering tools enhance identification of common and unique clusters or ORFs, highlighting features that could be used in generating primers for expression studies containing groups of organisms.

Genomics Tools
Genomics Tools

  • Multiple Sequence Alignment

  • Pairwise Sequence alignment

  • Creating and viewing taxonomic trees

  • Genome Alignment

  • Automated and Manual Genome Annotation

Integrated Databases
Integrated Databases

ERGO Database of 3000+ annotated genomes

KEGG Pathway Database

MetaCyc, EcoCyc, and BioCyc databases.

Gene Ontology

RefSeq

Swissprot

Uniprot

Cloud and On Premises Installations
Cloud and On Premises Installations

Access ERGO through our secure cloud from anywhere in the world. Your data is encrypted at all times; at rest and in transit. Private cloud and secure internal network installations are also available. Contact us for details.

Application Programmer Interface (API)
Application Programmer Interface (API)

ERGO's incredible proprietary database and toolset is now available via a REST API. Easily integrate ERGO with your existing tools and infrastructure.

Import/Export File Formats
Import/Export File Formats

Easily import and export standard genomics formats such as:

  • Genome Feature Format (GFF V2/V3)

  • FASTA

  • GenBank

  • CSV/Text

  • Variant Files (VCF/BCF)

    and others

Proven scientific results with ERGO.

ERGO has been cited hundreds of times from researchers all over the world.

Featured
Customer Publication, Microbiome, Metagenomics
Comparison of Yamuna (India) and Mississippi River (United States of America) bacterial communities reveals greater diversity below the Yamunotri Glacier
Customer Publication, Microbiome, Metagenomics
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Customer Publication, Microbiome, Metagenomics
Pathogenomics, Collaboration, Medical, Comparative Genomics, Genome Annotation, Transcriptomics, RNA-Seq, Grants and Collaborations
A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris
Pathogenomics, Collaboration, Medical, Comparative Genomics, Genome Annotation, Transcriptomics, RNA-Seq, Grants and Collaborations
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Pathogenomics, Collaboration, Medical, Comparative Genomics, Genome Annotation, Transcriptomics, RNA-Seq, Grants and Collaborations
Microbiome, Customer Publication, Pathogenomics
Zooming in on the intracellular microbiome composition of bacterivorous Acanthamoeba isolates
Microbiome, Customer Publication, Pathogenomics
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Microbiome, Customer Publication, Pathogenomics
Pathogenomics, Customer Publication
Borrelia nietonii sp. nov.: Relapsing Fever Spirochetes Transmitted By the Tick Ornithodoros hermsi Designated Previously as Borrelia hermsii Genomic Group II
Pathogenomics, Customer Publication
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Pathogenomics, Customer Publication
Customer Publication, Food & Agriculture
The quorum sensing peptide BlpC regulates the transcription of genes outside its associated gene cluster and impacts the growth of Streptococcus thermophilus
Customer Publication, Food & Agriculture
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Customer Publication, Food & Agriculture
Customer Publication, Plant
Whole-genome sequence and annotation of Penstemon davidsonii
Customer Publication, Plant
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Customer Publication, Plant
Customer Publication, Pathogenomics, Genome Assembly
De novo assembly of Roseomonas mucosa isolated from patients with atopic dermatitis
Customer Publication, Pathogenomics, Genome Assembly
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Customer Publication, Pathogenomics, Genome Assembly
Customer Publication, Comparative Genomics
Beyond rational—biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes
Customer Publication, Comparative Genomics
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Customer Publication, Comparative Genomics
Customer Publication, RNA-Seq, Synthetic Biology
Transcriptomics elucidates metabolic regulation and functional promoters in the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938
Customer Publication, RNA-Seq, Synthetic Biology
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Customer Publication, RNA-Seq, Synthetic Biology
Customer Publication, Industrial
Discovery of novel amino acid production traits by evolution of synthetic co-cultures
Customer Publication, Industrial
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Customer Publication, Industrial

 

ERGO is used by scientists worldwide.

“We have found the ERGO discovery system to be exceptionally useful tool for our metabolic engineering projects and expect that it will assist us in developing new production strains for higher and more cost effective production of biological compounds.”
— Dr. Thomas Haas, Director Science-to-Business Center Biotechnology at Evonik
“We are delighted to be working with Integrated Genomics ... The ERGO™ platform will enable us to further understand and exploit our thermophilic strains to their fullest potential to deliver the next generation of green biofuels.”
— Dr Steven Martin, Associate R & D Director at TMO
“The ERGO™ platform gives us a valuable and comprehensive resource for our genomics studies and provides a powerful data-mining environment for our scientists”
— Dr Barton Slatko, Senior Scientist in the Molecular Parasitology Division at NEB
“As DANONE is working on probiotics products, ERGO is a great database to help us to find probiotic functions in our strains.”
— Dr. Sophie Legrain-Raspaud, Team Leader in the Probiotic Gene identification group at the DANONE Research Center
ERGO News
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New ERGO Feature: Metabolomics Data Integration
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New ERGO Feature: MetaCyc/EcoCyc/BioCyc Pathway Database Integration
New ERGO Feature: MetaCyc/EcoCyc/BioCyc Pathway Database Integration
Read More →
You can create a Feature List from the Orthologs Table
New ERGO Feature: Feature Lists
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New ERGO Feature: Bulk Downloads
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New ERGO Feature: Functional Prediction for 16S Amplicon Sequencing data

We’ve added to ERGO’s rich suite of tools and workflows for 16S amplicon sequencing studies to include functional metagenome prediction utilizing Picrust2.

Read More →
PERMANOVA and Other New Features for ERGO Microbiome Analysis
PERMANOVA and Other New Features for ERGO Microbiome Analysis

Do the differences you see on the ordination plot represent a significant difference? This is one of the key questions researchers ask themselves. One way to determine significance is permutational multivariate analysis of variance (PERMANOVA), a statistical test commonly used in ecology settings [1]. ERGO uses the 'adonis' function in the R package vegan which provides functions for the analysis of ecology [2].

Read More →
New Ordination Methods for Microbiome Analysis in ERGO
New Ordination Methods for Microbiome Analysis in ERGO

Non-metric dimensional scaling attempts to closely represent pairwise dissimilarity between samples. It is a robust unconstrained ordination method that uses rank orders commonly used in ecology studies. Unlike many other ordination techniques NMDS iterates to find a solution that fits with an optimal stress value to the number of chosen dimensions. ERGO gives you a simple interface to choose the number of attempts, dimensions, along with an option to specify a previous best stress.

Read More →
Updates to Microbiome Analysis in ERGO
Updates to Microbiome Analysis in ERGO

Data mining and visualization just got easier in ERGO’s newest microbiome analysis update.

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New ERGO Feature: Violin Plots for Expression Analysis

We’ve added to ERGO’s rich visualizations with a new plot type: the violin plot. A violin plot is a way to visualize an underlying distribution of values (in our case, log fold change). Similar in utility to a box plot, a violin plot has a few advantages. Instead of just representing the median, quartiles, minimum and maximum, a violin plot uses a kernel density estimation algorithm to visualize the distribution of underlying points.

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Linear Discriminate (LEfSe) of Amplicon and Metagenome sequencing available in ERGO
Linear Discriminate (LEfSe) of Amplicon and Metagenome sequencing available in ERGO

ERGO’s [Overbeek et. all 2003] rich suite of tools and workflows to examine amplicon and metagenome sequencing now includes Linear Discriminate Analysis using LEfSe [Segata et. al 2010]. In ERGO, LEfSe (Linear discriminate analysis Effect Size) enables researchers to discover biomarkers that most likely explain the differences between selected experimental groups.

Read More →

Flyers and Info Sheets

View the ERGO 2.0 Flyer

View the ERGO 2.0 Flyer

 
Includes BioCycTM pathway/genome databases under license from SRI International.
Includes KEGGTM pathway/genome databases under license from Pathway Solutions, Inc.