Difference between revisions of "MaizeGDB and CoGe"
From CoGepedia
| Line 3: | Line 3: | ||
===[http://maizegdb.org MaizeGDB]'s genome browser link to CoGe's genome broswer, [[GenomeView]]=== | ===[http://maizegdb.org MaizeGDB]'s genome browser link to CoGe's genome broswer, [[GenomeView]]=== | ||
| − | [[Image:MaizeGDB-CoGe-link.png|Screen-shot of MaizeGDB with link to CoGe. http://gbrowse.maizegdb.org/cgi-bin/gbrowse/maize/?name=chr1:1000000..1200000]] | + | [[Image:MaizeGDB-CoGe-link.png|thumb|800px|center|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]]=== | ===[[GenomeView]] showing glyphs for genes linked to [[GEvo]]=== | ||
| − | [[Image:GenomeView-GEvo link Glyphs.png|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]] | + | [[Image:GenomeView-GEvo link Glyphs.png|thumb|800px|center|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]]=== | ===Getting a link to [[GEvo]]=== | ||
| − | [[Image:GenomeView-annotation-with-gevo-link.png|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]] | + | [[Image:GenomeView-annotation-with-gevo-link.png|thumb|800px|center|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=== | ===Automatically running [[GEvo]] with syntenic maize-sorghum regions pre-loaded=== | ||
===[[GEvo]]'s results=== | ===[[GEvo]]'s results=== | ||
Revision as of 14:06, 8 February 2010
Contents
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
