Informatics
Overview
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
Pathema: A Clade Specific NIAID BRC designed to support bio-defense and infectious disease research.
JCVI scientists in collaboration with the University of California, San Diego (UCSD), and Scripps Institution of Oceanography have built a s...
Celera Assembler can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing.
CMR is a free tool that allows researchers to access all of the publicly available bacterial genome sequences completed to date.
The NIH Human Microbiome Project (HMP) was initiated to help determine the core human microbiome, to understand the changes in the human mic...
In an effort to provide the tools of modern genomic science to researchers with prokaryotic genome sequences in need of annotation, JCVI has...
Enabling scientists to quickly provision cloud-based bioinformatics platforms such as Amazon EC2 and Eucalyptus.
The JCVI Microbial Sequence Center (MSC), sponsored by the National Institute for Allergies and Infectious Disease (NIAID), addresses the sc...
With the support of the Moore Foundation, we are sequencing, assembling, and auto-annotating the genomes of 165 marine microbes.
Store and apply naming rules to identify and correct syntactically incorrect protein names or to replace synonyms with preferred name.
MPIDB aims to collect and provide all known physical microbial interactions. Currently, 22,530 experimentally determined physical interactio...
TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFam, the fu...