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 28, 2013

Phylogenetic Analysis by Maximum Likelihood (PAML) Test performed on FleN, FleQ, FlhF orthologs and aeruginosa only orthologs

Gene	PAML outfile for orthologs	PAML outfile for aeruginosa
fleN	fleN PAML	aeruginosaPAML
fleQ	fleQ PAML	aeruginosa PAML
flhf	flhF PAML	aeruginosa PAML

To do:

1. Estimate genome tree using MrBayes and BEST (http://www.stat.osu.edu/~dkp/BEST/introduction/).
2. Analysis of positively selected genes using PAML and homozygosity analysis

Update: June 18, 2013

Ortholog aligning and phylogenetic tree material and methods

Protein ortholog data: fleN, fleQ, flhF    

1. 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> -clwstrict
   3. To create tree file run clustalW2 Usage >clustalw2 -infile= <Aligned_file> -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)