Pseudomonas population genomics: Difference between revisions

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imported>Rayrah
imported>Rayrah
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==Update: June 18, 2013==
==Update: June 18, 2013==
# Material and Methods
Ortholog Aligning and Phylogenetic Tree
## Protein ortholog data: [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105676&start=1583956&stop=1584798&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleN], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=104960&start=1187587&stop=1189059&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleQ], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105674&start=1582528&stop=1583817&replicon_id_reference=136&alphabet=protein&limit_to_species=false flhF]     
Material and Methods
## Protocol:
# Protein ortholog data: [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105676&start=1583956&stop=1584798&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleN], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=104960&start=1187587&stop=1189059&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleQ], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105674&start=1582528&stop=1583817&replicon_id_reference=136&alphabet=protein&limit_to_species=false flhF]     
### 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)
# Protocol:
### To align use [http://www.drive5.com/muscle/Alignment muscle] Usage: <code> >muscle -in <FASTA_File> -out <OUTPUTfilename> -clwstrict </code>
## 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 create tree file run [http://www.clustal.org/clustal2/ clustalW2] Usage <code>>clustalw2 -infile= <Aligned_file> -output= Phylip </code>  
## To align use [http://www.drive5.com/muscle/Alignment muscle] Usage: <code> >muscle -in <FASTA_File> -out <OUTPUTfilename> -clwstrict </code>
### To create tree run [http://www.r-project.org/ R] using following commands:
## To create tree file run [http://www.clustal.org/clustal2/ clustalW2] Usage <code>>clustalw2 -infile= <Aligned_file> -output= Phylip </code>  
####<code> setwd("<directory containing phylip files>")</code>
## To create tree run [http://www.r-project.org/ R] using following commands:
####<code> library ("ape")</code>  
###<code> setwd("<directory containing phylip files>")</code>
####<code> library ("phangorn")</code>
###<code> library ("ape")</code>  
####<code> <gene_name> = read.tree("<file_gene_name.phy>")</code>
###<code> library ("phangorn")</code>
####<code> <gene_name> = midpoint(gene_name)</code>
###<code> <gene_name> = read.tree("<file_gene_name.phy>")</code>
####<code> plot(<gene_name>)</code>
###<code> <gene_name> = midpoint(gene_name)</code>
###<code> plot(<gene_name>)</code>
{| class="wikitable"
{| class="wikitable"
! Gene !! Alignment !! Tree !! Notes  
! Gene !! Alignment !! Tree !! Notes  

Revision as of 21:23, 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

Ortholog Aligning and Phylogenetic Tree 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> -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)
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