DOE JGI Science Highlights: New tools for the IMG/M analysis system

Since the initial release of the Integrated Microbial Genomes with Microbiome samples (IMG/M) system in 2007 to support the comparative analysis of metagenomic data sets, DOE JGI researchers have made several updates in order to keep pace with the rapid increase in data set generation due to advances in sequencing technologies.

Victor Markowitz (left) and Nikos Kyrpides (right)

As reported by researchers led by DOE JGI’s Prokaryote Super Program Head Nikos Kyrpides and Chief Informatics Officer Victor Markowitz (who also leads the Biological Data Management and Technology Center at Lawrence Berkeley National Laboratory), new data analysis tools available to users include the ability to estimate the phylogenetic composition of a metagenome sample, as well as the ability to compare up to five user-selected metagenomes based on their BLAST hits. There are also “Abundance Profile” tools that allow users to compare the functional capabilities of metagenomes and genomes. The report was published online November 15, 2011 in Nucleic Acids Research. 

“Data sets from next generation sequencing technology platforms often result in million sequences rendering storing and accessing of data in the standard relational data bases

 inefficient,” the team wrote in their report. “As we expect an exponential growth of the size of metagenome data sets by these platforms, we are devising new data management techniques for organizing metagenome data in support of effective analysis.”

The IMG/M system integrates metagenome data sets with isolate microbial genomes from the IMG system. The current version of IMG/M contains 224 metagenome data sets from nearly 90 studies, a fraction, the team noted, of the metagenome data sets being annotated and reviewed through the IMG Expert Review (IMG/ER) system.