Difference between revisions of "Running P-POD orthology tool on the reference genomes gene set (Retired)"

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The current plan is to start with the gp2protein files, which we at Princeton will use to retrieve the actual protein sequences and generate fasta files.  We will use the following files from the GO site:
The current plan is to start with the gp2protein files, which we at Princeton will use to retrieve the actual protein sequences and generate fasta files.  We will use the following files from the GO site:


     * Arabidopsis thaliana gp2protein.tair.gz
     * Arabidopsis thaliana: gp2protein.tair.gz
     * Caenorhabditis elegans  gp2protein.wb.gz
     * Caenorhabditis elegans: gp2protein.wb.gz
     * Danio rerio gp2protein.zfin.gz
     * Danio rerio: gp2protein.zfin.gz
     * Dictyostelium discoideum gp2protein.dictyBase.gz
     * Dictyostelium discoideum: gp2protein.dictyBase.gz
     * Drosophila melanogaster gp2protein.fb.gz
     * Drosophila melanogaster: gp2protein.fb.gz
     * Homo sapiens gp2protein.human.gz
     * Homo sapiens: gp2protein.human.gz
     * Mus musculus gp2protein.mgi.gz
     * Mus musculus: gp2protein.mgi.gz
     * Saccharomyces cerevisiae gp2protein.sgd.gz
     * Saccharomyces cerevisiae: gp2protein.sgd.gz
     * Schizosaccharomyces pombe gp2protein.genedb_spombe.gz
     * Schizosaccharomyces pombe: gp2protein.genedb_spombe.gz
     * Rattus norvegicus  gp2protein file from RGD (pending)
     * Rattus norvegicus: gp2protein file from RGD (pending)
 
     * Escherichia coli:  Uniprot file
And the Uniprot file will be used for these species:
     * Gallus gallus:  Uniprot file
 
     * Escherichia coli    
     * Gallus gallus

Revision as of 11:40, 18 January 2008

The current plan is to start with the gp2protein files, which we at Princeton will use to retrieve the actual protein sequences and generate fasta files. We will use the following files from the GO site:

   * Arabidopsis thaliana: gp2protein.tair.gz
   * Caenorhabditis elegans:  gp2protein.wb.gz
   * Danio rerio: gp2protein.zfin.gz
   * Dictyostelium discoideum: gp2protein.dictyBase.gz
   * Drosophila melanogaster: gp2protein.fb.gz
   * Homo sapiens: gp2protein.human.gz
   * Mus musculus: gp2protein.mgi.gz
   * Saccharomyces cerevisiae: gp2protein.sgd.gz
   * Schizosaccharomyces pombe: gp2protein.genedb_spombe.gz
   * Rattus norvegicus:  gp2protein file from RGD (pending)
   * Escherichia coli:  Uniprot file
   * Gallus gallus:  Uniprot file