Pseudomonas population genomics

Projects

1. Build a local genome database
   1. Database schema:
      1. "genome": genome_id, strain_name, ncbi_taxid
      2. "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name
      3. "orth_orf": orth_orf_id, locus_name, genome_id, orth_class
   2. Parsing scripts
      1. Rayees Parsing code, requires that you remove columns 9-27 using bash command: cut -c 1-8 (I will write a bash script that does this and runs the program) https://www.dropbox.com/s/lpxxbkxeyw7frrn/parser.pl
   3. Database loading scripts
2. Molecular Evolution of flagellum genes
   1. Download orthologs
   2. Reconstruct phylogenetic tree
   3. Run PAML tests

Benchmark: June 11, 2013

1. Finish parsing the genome files to upload the "orf" table (Raymond & Rayees)
   1. Rayees Parsed genome files: https://www.dropbox.com/sh/k0zktvvmv39op9i/1zBercEky8
2. Parsing the ortholog file to upload the "orth_orf" table (Raymond)
3. Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees)