MaizeGDB and CoGe

Overview

MaizeGDB is linked to CoGe's through its genome browser. A link to CoGe will be shown at the top of the browser when viewing a genomic region from the maize genome assembly (i.e. pseudomolecules). This link will take you to the same region in CoGe's GenomeView. GenomeView will automatically find maize genes with annotations that link to GEvo for syntenic gene sets with sorghum, and show those genes with special glyphs. When you view the annotations for these glyphs (by clicking on them), there will be a link to GEvo. When clicked on, these GEvo links will launch GEvo with the syntenic maize-sorghum regions pre-loaded and automatically start a GEvo analysis using blastz.

MaizeGDB's genome browser link to CoGe's genome broswer, GenomeView

Screen-shot of MaizeGDB with link to CoGe. http://gbrowse.maizegdb.org/cgi-bin/gbrowse/maize/?name=chr1:1000000..1200000

GenomeView showing glyphs for genes linked to GEvo

Screen-shot of GenomeView showing GEvo link glyphs. http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=1100000&dsgid=8054&chr=1&sl=1

Getting a link to GEvo

GenomeView with annotation dialog box shown for a GEvo link glyph. http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=1100000&dsgid=8054&chr=1&sl=1

Automatically running GEvo with syntenic maize-sorghum regions pre-loaded

GEvo running a maize-sorghum syntenic analysis automatically. Genomic regions (400kb) have been preloaded in the sequence submission boxes. http://tinyurl.com/yhgnu8a