Running P-POD orthology tool on the reference genomes gene set (Retired)
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.
The initial plan is to do all v. all BLAST, OrthoMCL, clustalW, then PHYLIP, as described here. 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.