Difference between revisions of "Syntenic gene sets"
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| − | + | Syntenic gene sets are sets of genes located in [[syntenic regions]] (genomic regions derived from the same ancestral genomic region) within and across genomes. These genes are usually in a [collinear gene order] and are used as evidence that the regions are syntenic. | |
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| + | ==How to generate syntenic gene sets with links to [[GEvo]]== | ||
| + | [[SynMap]] allows you to compare any two genomes. Its output includes a text file of all identified syntenic gene pairs and links to [[GEvo]]. | ||
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| + | ==Published Syntenic Gene Sets== | ||
| + | These lists are usually from publications in MS Excel format and provide links to populate the sequence submission form in [GEvo], CoGe's tool for analyzing multiple genomic regions. These links allow you to quickly start comparing syntenic regions of interest. | ||
Papaya, Poplar, and Grape: CoGe with Rosids.] Plant Physiol. 148: 1772 Lyons et al. | Papaya, Poplar, and Grape: CoGe with Rosids.] Plant Physiol. 148: 1772 Lyons et al. | ||
| − | [http://synteny.cnr.berkeley.edu/CoGe/data/distrib/SI2_At-Cp4.xls Arabidopsis thaliana - Carica papaya]: At has had two tetraploidies while Cp has had none. (Prepared by the Paterson lab at the Plant Center at the University of Georgia and modified by the Freeling lab to include GEvo links. From: [http://www.plantphysiol.org/cgi/content/abstract/148/4/1772 Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups) | + | [http://synteny.cnr.berkeley.edu/CoGe/data/distrib/SI2_At-Cp4.xls Arabidopsis thaliana - Carica papaya]: At has had two tetraploidies while Cp has had none. (Prepared by the Paterson lab at the Plant Center at the University of Georgia and modified by the Freeling lab to include GEvo links. From: [http://www.plantphysiol.org/cgi/content/abstract/148/4/1772 Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups].) |
| − | [http://synteny.cnr.berkeley.edu/CoGe/data/distrib/SI1_At-Cp-Vv-2Pt_GEvo_links.xls Arabidopsis thaliana - Carica papaya - Vitis vinifera - Populus trichocarpa(2x)]: This list contains both syntenic regions for poplar from its most recent genome duplication event, but only a single for Arabidopsis. | + | [http://synteny.cnr.berkeley.edu/CoGe/data/distrib/SI1_At-Cp-Vv-2Pt_GEvo_links.xls Arabidopsis thaliana - Carica papaya - Vitis vinifera - Populus trichocarpa(2x)]: This list contains both syntenic regions for poplar from its most recent genome duplication event, but only a single for Arabidopsis. From: [http://www.plantphysiol.org/cgi/content/abstract/148/4/1772 Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups |
Revision as of 19:29, 8 February 2010
Syntenic gene sets are sets of genes located in syntenic regions (genomic regions derived from the same ancestral genomic region) within and across genomes. These genes are usually in a [collinear gene order] and are used as evidence that the regions are syntenic.
How to generate syntenic gene sets with links to GEvo
SynMap allows you to compare any two genomes. Its output includes a text file of all identified syntenic gene pairs and links to GEvo.
Published Syntenic Gene Sets
These lists are usually from publications in MS Excel format and provide links to populate the sequence submission form in [GEvo], CoGe's tool for analyzing multiple genomic regions. These links allow you to quickly start comparing syntenic regions of interest.
Papaya, Poplar, and Grape: CoGe with Rosids.] Plant Physiol. 148: 1772 Lyons et al. Arabidopsis thaliana - Carica papaya: At has had two tetraploidies while Cp has had none. (Prepared by the Paterson lab at the Plant Center at the University of Georgia and modified by the Freeling lab to include GEvo links. From: Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups.)
Arabidopsis thaliana - Carica papaya - Vitis vinifera - Populus trichocarpa(2x): This list contains both syntenic regions for poplar from its most recent genome duplication event, but only a single for Arabidopsis. From: [http://www.plantphysiol.org/cgi/content/abstract/148/4/1772 Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups
