[Gmod-schema] example data for comparative genomics analysis

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[Gmod-schema] example data for comparative genomics analysis

Kara Dolinski
Hi everyone,

We doing some comparative sequence analysis, and would like to put all this in a database and turn it into a publicly accessible resource.  We are planning on using the GMOD database package for this.  Before we spent a bunch of time poring over the schema, writing scripts that load the BLAST results, etc, I figured I'd see if anyone else has done something similar, and had a sample database and/or loading scripts, etc to save us some time.

We're doing something relatively straightforward, using BLAST and ORTHOMCL to generate protein families, generating alignments of the families with ClustalW, then generating phylogenetic trees using PHYLIP to generate nice images of the rooted trees.  So, we're looking for examples of a GMOD/chado database that contains any/all of these types of data to help figure out where all the bits of info would go in the companalysis and other schema modules.   Scripts that load the data into the database would be very much welcome as well.  :)

Thanks,
Kara

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Kara Dolinski, Ph.D.

Genome Databases/SGD Princeton colony

Lewis-Sigler Institute for Integrative Genomics

Princeton University

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