Pseudomonas population genomics

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Revision as of 22:36, 3 June 2013 by imported>Weigang (Created page with "==Projects== #Build a local genome database ## Database schema: ### "genome": genome_id, strain_name, ncbi_taxid ### "orf": genome_id, locus_tag, start, stop, strand, genome_...")
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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
    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)
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