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

From GO Wiki
Jump to navigation Jump to search
Line 1: Line 1:
'''Input sequences'''
'''Input sequences'''


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 will be used to generate fasta files.  We will use the following files from the GO site:


     * Arabidopsis thaliana: gp2protein.tair.gz
     * Arabidopsis thaliana: gp2protein.tair.gz
Line 28: Line 28:
     * Gallus gallus:  Uniprot file
     * Gallus gallus:  Uniprot file


Questions still pending:
Notes: Uniprot and/or NCBI might be the source of the identifiers.  Currently, not all databases provide complete sets of both, so we need to retrieve from both databases as appropriate.  In the future, it would be great if all the data providers could provide both as a service to users.  For our purposes, it would be useful to provide links to both resources from the web interfaces.


Will all of these files have both Uniprot and NCBI identifiers available?  This would be great because it would allow us to provide useful links to both resources from the results.
Related to the above:  should we retrieve the sequences from Uniprot or NCBI?  Notes on identifiers available for each species are above.


We will download the sequences at the end of January based on whatever files are available and will begin the run then.
We will download the sequences at the end of January based on whatever files are available and will begin the run then.

Revision as of 15:16, 29 January 2008

Input sequences

The current plan is to start with the gp2protein files, which will be used to generate fasta files. We will use the following files from the GO site:

   * Arabidopsis thaliana: gp2protein.tair.gz
    RefSeq (NCBI) identifiers / NCBI need to be used because coverage for Uniprot mappings is not 100%.
   * 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

Notes: Uniprot and/or NCBI might be the source of the identifiers. Currently, not all databases provide complete sets of both, so we need to retrieve from both databases as appropriate. In the future, it would be great if all the data providers could provide both as a service to users. For our purposes, it would be useful to provide links to both resources from the web interfaces.


We will download the sequences at the end of January based on whatever files are available and will begin the run then.

Analysis pipeline

The initial plan is to do all v. all BLAST, OrthoMCL, clustalW, then PHYLIP, as described here[1]. We will also make the BLAST results available separately.

Once we get at least the initial run finished, we will explore alternative methods and combinatorial approaches.