Difference between revisions of "Ancestral angiosperm genomes"
From CoGepedia
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[[File:Screen shot 2012-06-18 at 10.51.11 AM.png|thumb|center|800px|Phylogeny of the Angiosperms with polyploidy events marked. Branch lengths are meaningless.]] | [[File:Screen shot 2012-06-18 at 10.51.11 AM.png|thumb|center|800px|Phylogeny of the Angiosperms with polyploidy events marked. Branch lengths are meaningless.]] | ||
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| + | ==Ancestral Eurosid== | ||
| + | # Data generated by Chungfang Zheng | ||
| + | # Procedure for generating ancestral genome: | ||
| + | ## Take ancestral ortholog sets from grape/chocolate/peach | ||
| + | ## Use the ortholog gene from first grape, then chocolate, then peach (if data is missing) | ||
| + | ## Extract CDS sequence from CoGe | ||
| + | ## Reverse complement if necessary | ||
| + | ## Print sequence | ||
| + | ## Pad with 1000 "N"s between coding sequence | ||
| + | |||
| + | Link to ancestral genome: http://genomevolution.org/CoGe/OrganismView.pl?oid=38348 | ||
| + | |||
| + | ===Syntenic dotplots=== | ||
| + | |||
| + | [[Eurosid Ancestor to Eurosid Ancestor]] | ||
| + | |||
| + | [[Eurosid Ancestor to Grape]] | ||
| + | |||
| + | [[Eurosid Ancestor to Amborella]] | ||
Revision as of 12:18, 18 June 2012
Ancestral Eurosid
- Data generated by Chungfang Zheng
- Procedure for generating ancestral genome:
- Take ancestral ortholog sets from grape/chocolate/peach
- Use the ortholog gene from first grape, then chocolate, then peach (if data is missing)
- Extract CDS sequence from CoGe
- Reverse complement if necessary
- Print sequence
- Pad with 1000 "N"s between coding sequence
Link to ancestral genome: http://genomevolution.org/CoGe/OrganismView.pl?oid=38348
