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:July 23, 2013

Pars and Dollop Parsimony Output

Update:July 22, 2013

Ld_hat results

Data	Number of Genes
No PA7	10
PA7	10
No PA7	50

Update:July 17, 2013

Phylip dollop parsimony tree based on an matrix of ortholog changes

parsimony output

Update: July 16, 2013

Treefiles based on aligned orthologs

number of genes used	Method	treefile
100	FASTTREE	treefile
100	FASTTREE	Treefile 2
all orthologs	Phylip	treefile_phylip

FleN, FleQ, Flhf unique strains

Gene	alignment	tree
fleN	fleN unique align
fleQ	fleQ unique align
flhf	flhF unique align

To do:

1. Create pipeline
2. LD_Hat w/ 10 genes excluding and including PA7

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
fleN	fleN PAML
fleQ	fleQ PAML
flhf	flhF-corrected 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)