Pseudomonas population genomics

From QiuLab
Revision as of 17:16, 11 June 2013 by imported>Rayrah (→‎Projects)
Jump to navigation Jump to search

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 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)
  2. Parsing the ortholog file to upload the "orth_orf" table (Raymond)
  3. Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees)