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

Update: June 18, 2013

1. Material and Methods
   1. Protein ortholog data: fleN, fleQ, flhF
   2. Protocol:
      1. Fasta headers are too long for tree, run: rename.pl to shorten names. Usage: >rename.pl <FASTA_file> > <OUTPUTfilename.fas> (will rewrite script to create automatic output file)
      2. To align use muscle Usage: >muscle -in <FASTA_File> -out <OUTPUTfilename.aln> -clwstrict
      3. To create tree file run clustalW2 Usage >clustalw2 -infile= <Aligned_file.aln> -output= Phylip
      4. To create tree run R using following commands:
         1. setwd("<directory containing phylip files>")
         2. library ("ape")
         3. library ("phangorn")
         4. <gene_name> = read.tree("<file_gene_name.phy>")
         5. <gene_name> = midpoint(gene_name)
         6. plot(<gene_name>)

Gene	Alignment	Tree	Notes
fleN	fleN pep alignment		Conserved Domain
fleQ	fleQ pep alignment		Conserved Domain
flhf	flhF pep alignment		Conserved Domain

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)