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Home Publications White papers
White papers

Random Community Genomics (metagenomics) - White Paper

The random community genomics white paper was written by Rob in the spring of 2006 while traveling around Europe for meetings. You'll notice that some of the problems have been solved, but many have been ignored!

Random community genomics, sequencing whole DNA without growing the microbes or cloning their DNA is now a reality. Our group, alone, has sequenced in excess of 850 M bp of DNA from environmental samples. Sample preparation and sequencing is very cheap and easy, costing less than $500 per million bp. The major limitation towards the advancement of our understanding of environmental genomics is no longer our ability to see the DNA. It is the lack of access to high-performance computing. Once the technologies and techniques that are being used be selected labs today become commonplace, there will be overwhelming demand for computational power beyond anything that is readily available.

Random community genomics, sequencing whole DNA without growing the microbes or
cloning their DNA is now a reality. Our group, alone, has sequenced in excess of 850 M bp of
DNA from environmental samples. Sample preparation and sequencing is very cheap and easy,
costing less than $500 per million bp.
The major limitation towards the advancement of our understanding of environmental
genomics is no longer our ability to see the DNA. It is the lack of access to high-performance
computing.
Once the technologies and techniques that are being used be selected labs today become
commonplace, there will be overwhelming demand for computational power beyond anything
that is readily available.

You can download the pdf (0.3 MB).


 

Automated analysis of ARISA data using ADAPT system - White Paper

This white paper was written by Robert in 2008 while working on different community profiling projets that combined microbiolgy and computer science.

The white paper describes a computational system consisting of the database ADAPTdb and the program ADAPT for the analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) data sets. ARISA is a method for analyzing the composition of microbial communities that is both faster and cheaper than other community profiling techniques. In an application example, we describe the use of the tool for an unpublished data set and compare the results to work previously published using different analysis methods. Although there have been many papers until 2008 that used ARISA to analyze community samples, there were none that described computational approaches that allow the automatic analysis of the raw data sets. We have taken the manual process, automated it, and developed a web-based program for the automatic analysis, including taxonomic classifications, as well as autotrophic/heterotrophic and pathogenic/non-pathogenic comparisons.

You can download the pdf (1.4 MB).