Pseudomonas population genomics

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Revision as of 17:33, 16 July 2013 by imported>Rayrah (→‎Update: July 16, 2013)
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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
      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 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

Flen unique.png

fleQ fleQ unique align Fleq unique.png
flhf flhF unique align Flhf unique.png

To do:

  1. Create pipeline

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 Flen.png Conserved Domain
fleQ fleQ pep alignment Fleq.png Conserved Domain
flhf flhF pep alignment Flhf.png 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)