The Wold Lab BioHub Cory Tobin

Collaborators Brandon King Joe Roden Diane Trout Dr. Barbara

Goal Standardize the relationship between biological data Integrate all of the data seamlessly Provide novel methods to search for and analyze data

Adapted from

My Contribution Implement a database for homology data

Background Species A Species B Paralogs Orthologs The more general term is “homology” Gene

Requirements Be more accurate and flexible than HomoloGene Work in real time Make sense of HomoloGene’s misleading data

Rationale Gene They are similar Gene HomoloGene BioHub They are related like this

Rationale Continued Human Genome Mouse Genome Seq ASeq B HomoloGene would BLAST seq A against mouse and determine that seq C is an ortholog of seq A. Seq C HomoloGene would also BLAST seq B against mouse and detrmine that seq C is an ortholog of seq B. BioHub will BLAST seq A against mouse, find seq C, then BLAST C back against human to see if there are any better matches. It will find seq B to be better.

Methods Design data relationships that make sense biologically Generate the low-level database interaction code Parse and load HomoloGene’s data into our database Write biologically useful functions Create a web-based interface for easy use

Materials ArgoUML – Design Aid Pymerase – Design Implementation PostgreSQL – Database HomoloGene – Data Source Python – Programming Language

Current State Design data relationships that make sense biologically Generate the low-level database interaction code Parse and load HomoloGene’s data into our database Write biologically useful functions Create a web-based interface for easy use

Example Usage Sequence of Interest …GGATACAAAATTCCTC… Are there any known genes in this sequence? acetyl - coenzyme A dehydrogenase ( Human ) (cont.)

acetyl - coenzyme A dehydrogenase ( Human ) Are there any homologs? Mouse Rat Mosquito Fruit fly Nematode (cont.)

How are those genes related?

Where do you want to go?

More Info BioHubwoldlab.caltech.edu / biohub HomoloGenewww.ncbi.nlm.nih.gov Pythonpython.org Pymerasepymerase.sf.net PostgreSQLpostgresql.org