Cbcb:Pop-Lab:Ted-Report
Summer 2009 Goals
- Research traditional approaches taken to gene-level analysis of metagenomic data
- Critically evaluate the traditional approaches in general and in the context of current Pop Lab projects
- Identify portions of the analysis that can be automated
- Develop scalable tools to do the automated analysis
May 15, 2009
- Read VisANT paper and user manual[1]. Determined VisANT will work for manual metabolic pathway analysis of even large scale data sets and can be automated by running in "Batch Mode".
- Need to read about FastHMM[2]
- Still need to make "Welcome Wiki" for n00bs (read: new members)
May 22, 2009
- Made Welcome Wiki
- Read metagenomics papers
- Determined that VisANT can be used with Bo's data by importing it as MicroArray data
May 29, 2009
- Took an early Summer vacation last weekend:
- Drove to NC to see friend graduate with BS' in CS & Physics
- Went sailing for the first time at girlfriends' parents' place in VA
- Refined Welcome Wiki
- Read metagenomics/pathway reconstruction/analysis papers
- Organized reading group for Palsson Systems Bio book
June 5, 2009
- Read metagenomics/pathway reconstruction/analysis papers and first two chapters of Palsson book.
- Currently building test set for incorporation of Phymm into metagenomics pipeline.
- A single archaeal genome was chosen from the findings of Mihai's 2006 Science paper analyzing the human distal gut.
- Two pairs of bacterial genomes were chosen for the test set using columns on the NCBI RefSeq Complete Genomes website[3]:
- The pairs of bacterial genomes were taken from the Groups: Bacteroidetes/Chlorobi and Firmicutes because they are the two most predominant groups present in the human gut.
- I chose genomes with a complete set of NCBI Tools available.
- After this I attempted to choose genomes with significantly different GC content.
- Finally, preference was given to organisms I recognized from gut microbiome papers/discussions, or failing that, just a really awesome name.
- The final list is:
- Methanobrevibacter_smithii_ATCC_35061 (archaea)
- Bacteroides fragilis NCTC 9343 (bacteroidetes)
- Porphyromonas gingivalis W83 (bacteroidetes)
- Aster yellows witches'-broom phytoplasma AYWB (firmicutes)
- Bacillus subtilis subsp. subtilis str. 168 (firmicutes)