Difference between revisions of "MaizeGDB and CoGe"
From CoGepedia
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===[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|thumb|800px|center|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. View can be regenerated at: 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|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]] | + | [[Image:GenomeView-GEvo link Glyphs.png|thumb|800px|center|Screen-shot of GenomeView showing GEvo link glyphs. View can be regenerated at: 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|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]] | + | [[Image:GenomeView-annotation-with-gevo-link.png|thumb|800px|center|GenomeView with annotation dialog box shown for a GEvo link glyph. View can be regenerated at: 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=== | ||
| − | [[Image:GEvo-running-maize-sorghum.png|thumb|800px|center|GEvo running a maize-sorghum syntenic analysis automatically. Genomic regions (400kb) have been preloaded in the sequence submission boxes. http://tinyurl.com/yhgnu8a]] | + | [[Image:GEvo-running-maize-sorghum.png|thumb|800px|center|[[GEvo]] running a maize-sorghum syntenic analysis automatically. Genomic regions (400kb) have been preloaded in the sequence submission boxes. Analysis can be run at: http://tinyurl.com/yhgnu8a]] |
===[[GEvo]]'s results=== | ===[[GEvo]]'s results=== | ||
| + | [[Image:GEvo-maize-sorghum.png|thumb|800px|center|[[GEvo]] results from a maize-sorghum sytnenic analysis. Lines have been drawn connecting regions of sequence similarity showing ~5 collinear pairs of genes. This is evidence that the regions are syntenic. Results can be regenerated at: http://tinyurl.com/yhgnu8a]] | ||
Revision as of 14:15, 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. View can be regenerated at: 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. View can be regenerated at: 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. View can be regenerated at: 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. Analysis can be run at: http://tinyurl.com/yhgnu8a
GEvo's results
GEvo results from a maize-sorghum sytnenic analysis. Lines have been drawn connecting regions of sequence similarity showing ~5 collinear pairs of genes. This is evidence that the regions are syntenic. Results can be regenerated at: http://tinyurl.com/yhgnu8a
