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swap out 'bash' for 'make' for generating protien database
bash is not the best solution, make is an alternative with minimal complexity
Revise method of matching query proteins to database for set-comparison
See hmmer for gene detection from database
check out OrthoMCL for clustering COGs
verify COG assignments for multiple hits and ensure that COG clusters are not being merged
Evaluate set-comparison predictor
- confirm CAG (Helicobacter pylori 26695) island can be picked from a large set of related genomes
- look into wild pseudomonas**, ecoli, salmonella species datasets for effectiveness
- find islands defined before islandpath to evaluate gi edge detection
- see buster:/data/NCBI_genomes/curated/ for genomes annotated with GIs, start with LESb58 genome
- create gene database for CAG and search helico genomes. check https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001069 for cag caveats
Implement gene blacklist for set-comparison
See islandpath paper (Will Hsiao) has list of genes that would want to filter out of islands
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