Bioinformatics Research Group

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Presentation transcript:

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

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.

Comparative Genome Browser Display

Ortholog-Links Can be stored as DBLINKS on gene frames http://bioinformatics.ai.sri.com/ptools/ortholog-link- setup.html Problem when many PGDBs: grows as N2 Ortholog-Link MySQL DB is used for BioCyc WWW site Contact ptools-support@ai.sri.com for setup

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*