1. Bioinformatics Research Group
Orthologs Internals
Markus Krummenacker
Bioinformatics Research Group
SRI, International
August 26th, 2009

2. Comparative Genome Browser
To enter, in Gene page, click on “Align in Multi- Genome Browser”
“Select Allowed Organisms” for what to compare to
Comparison only works when Ortholog-Links are present
The selected gene is centered, and aligned with Orthologs in the other PGDBs
Colors mean shared Orthologs. A dozen colors are reused.

3. Comparative Genome Browser Display

4. Ortholog-Links Can be stored as DBLINKS on gene frames
setup.html
Problem when many PGDBs: grows as N2
Ortholog-Link MySQL DB is used for BioCyc WWW site
Contact for setup

5. Ortholog-Links MySQL Server
At SRI, we dump out orthologs as a tab-delimited flat- file, from CMR loaded into BioWarehouse
Flat file format is: GENEID1 GENEID2 ORGID1 ORGID2 P-Value
Load flatfiles into MySQL, using
(init-ortho-link-db “/file/path/to/flatfiles/”)
Setup of connection parameters to MySQL server.
*ortholog-link-host*
*ortholog-link-database*
*ortholog-link-username*
*ortholog-link-passwords*