JCVI: Research / Platforms / Informatics
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Informatics is at the heart of any genomics research enterprise as it is critical for the analysis of large data-sets. The challenge in genomics is assembling in the correct order the thousands to billions of pieces of random DNA sequence that is generated by the whole genome shotgun technique. This is where our informatics experts come into play. These scientists develop the software, mathematical tools, and databases to assemble and analyze these genomes. In fact, as more and more genomes are sequenced and as we begin to explore whole environments at the DNA level, the need for computational resources continues to grow exponentially.

At the JCVI one of our largest teams is Informatics. This group includes software engineers and applied and research bioinformatics experts. Starting with his team at the National Institutes of Health (NIH) to the formation of The Institute for Genomic Research (TIGR) and today at the JCVI, Dr. Venter has long known that computational resources are the critical component for genomic research. Our informatics team has enabled us to do everything from uncover more than six million new genes in the world's oceans to creating internationally renowned databases and tools to study the genomes of hundreds of pathogens, plants, and mammalian genomes.

Project Highlights

Bioinformatics Resource Center (BRC)

Pathema: A Clade Specific NIAID BRC designed to support bio-defense and infectious disease research.


CABOG assembles long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing.


JCVI scientists in collaboration with the University of California, San Diego (UCSD), and Scripps Institution of Oceanography have built a...

Comprehensive Microbial Resource (CMR)

CMR is a free tool that allows researchers to access all of the publicly available bacterial genome sequences completed to date.

FLOCK: Flow Cytometry Clustering without K

FLOCK is a computational algorithm to identify cell populations within multi-dimensional flow cytometry (FCM) data. It has been implemented...

Human Microbiome Project (HMP)

The NIH Human Microbiome Project (HMP) was initiated to help determine the core human microbiome, to understand the changes in the human...

Influenza Research Database (IRD)

IRD is a publicly available, NIAID-sponsored one-stop database and analysis resource that supports influenza research. IRD integrates data...

JCVI Annotation Service

In an effort to provide the tools of modern genomic science to researchers with prokaryotic genome sequences in need of annotation, JCVI...

JCVI Cloud BioLinux

Enabling scientists to quickly provision cloud-based bioinformatics platforms such as Amazon EC2 and Eucalyptus.


The metadata-driven comparative analysis tool for sequences (meta-CATS) rapidly identifies sequence variations that significantly correlate...


An open source suite of tools for high-performance comparative metagenomics.

Moore Foundation Marine Microbial Genome Sequencing Project

With the support of the Moore Foundation, we are sequencing, assembling, and auto-annotating the genomes of 165 marine microbes.

Protein Naming Utility

Store and apply naming rules to identify and correct syntactically incorrect protein names or to replace synonyms with preferred name.

The Microbial Protein Interaction Database

MPIDB aims to collect and provide all known physical microbial interactions. Currently, 22,530 experimentally determined physical...


TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFam, the...

Viral Ortholog Clustering

A modification to the OrthoMCL algorithm improves the performance of ortholog clustering for viral proteins.

Virus Pathogen Resource (ViPR)

ViPR is a publicly available, NIAID-sponsored one-stop database and analysis resource that supports the research of viral pathogens in the...

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