Pseudomonas population genomics
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Projects
- Build a local genome database
- Database schema:
- "genome": genome_id, strain_name, ncbi_taxid
- "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name
- "orth_orf": orth_orf_id, locus_name, genome_id, orth_class
- Parsing scripts
- 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
- Rayees Parsing code, requires that you remove columns 9-27 using bash command:
- Database loading scripts
- Database schema:
- Molecular Evolution of flagellum genes
- Download orthologs
- Reconstruct phylogenetic tree
- Run PAML tests
Benchmark: June 11, 2013
- Finish parsing the genome files to upload the "orf" table (Raymond & Rayees)
- Parsing the ortholog file to upload the "orth_orf" table (Raymond)
- Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees)