Pseudomonas population genomics: Difference between revisions

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imported>Rayrah
imported>Rayrah
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## Protocol:
## Protocol:
### Fasta headers are too long for tree, run: [https://www.dropbox.com/s/x2p4joeqg7omfub/rename.pl rename.pl] to shorten names. Usage:<code> >rename.pl <FASTA_file> > <OUTPUTfilename.fas> </code> (will rewrite script to create automatic output file)
### Fasta headers are too long for tree, run: [https://www.dropbox.com/s/x2p4joeqg7omfub/rename.pl rename.pl] to shorten names. Usage:<code> >rename.pl <FASTA_file> > <OUTPUTfilename.fas> </code> (will rewrite script to create automatic output file)
### To align use [http://www.drive5.com/muscle/Alignment muscle] Usage: <code> >muscle -in <FASTA_File> -out <OUTPUTfilename.aln> -clwstrict </code>
### To align use [http://www.drive5.com/muscle/Alignment muscle] Usage: <code> >muscle -in <FASTA_File> -out <OUTPUTfilename> -clwstrict </code>
### To create tree file run [http://www.clustal.org/clustal2/ clustalW2] Usage <code>>clustalw2 -infile= <Aligned_file.aln> -output= Phylip </code>  
### To create tree file run [http://www.clustal.org/clustal2/ clustalW2] Usage <code>>clustalw2 -infile= <Aligned_file.aln> -output= Phylip </code>  
### To create tree run [http://www.r-project.org/ R] using following commands:
### To create tree run [http://www.r-project.org/ R] using following commands:

Revision as of 21:21, 18 June 2013

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> -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 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)