Difference between revisions of "Tutorials"
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*[[Potato version 1 | Plant example]] | *[[Potato version 1 | Plant example]] | ||
=== Genome Comparison and Analysis using SynMap and GEvo === | === Genome Comparison and Analysis using SynMap and GEvo === | ||
| − | [[Analysis of variations found in genomes of Escherichia coli strain K12 DH10B and strain B REL606 using SynMap and GEvo analysis]] | + | *[[Analysis of variations found in genomes of Escherichia coli strain K12 DH10B and strain B REL606 using SynMap and GEvo analysis]] |
| − | [[Maize Sorghum Syntenic dotplot]] Since these lineages diverged ~11 MYA, maize has had a whole genome duplication event; prior to their divergence the lineage had a whole genome duplication event. Using SynMap's synonymous mutation overlay, it is easy to determine which syntenic regions are derived from the pre-grass whole genome duplication event or the one specific to maize. | + | *[[Maize Sorghum Syntenic dotplot]] Since these lineages diverged ~11 MYA, maize has had a whole genome duplication event; prior to their divergence the lineage had a whole genome duplication event. Using SynMap's synonymous mutation overlay, it is easy to determine which syntenic regions are derived from the pre-grass whole genome duplication event or the one specific to maize. |
===Finding Inversions=== | ===Finding Inversions=== | ||
| − | [[Bacteria Genomic Inversion]] This example shows an [[inversion]] between substrains of Escherichia coli K12, DH10B and W3110. | + | *[[Bacteria Genomic Inversion]] This example shows an [[inversion]] between substrains of Escherichia coli K12, DH10B and W3110. |
=== Ortholog identification and conserved noncoding sequence (CNS) analysis === | === Ortholog identification and conserved noncoding sequence (CNS) analysis === | ||
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{{reflist}} | {{reflist}} | ||
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| + | ===Finding rarely and frequently used codons=== | ||
| + | *This is very straight forward using [[OrganismView]]. Just find your organism and [[generate a codon usage table]]. | ||
== Videos == | == Videos == | ||
Revision as of 17:21, 28 December 2009
Here you can find tutorials informing you how to get the most out of CoGe's tools.
Contents
Original tutorials
You can find a list of CoGe's old tutorials here.
Text
What to do with a genome in the early stages of assembly?
Genome Comparison and Analysis using SynMap and GEvo
- Maize Sorghum Syntenic dotplot Since these lineages diverged ~11 MYA, maize has had a whole genome duplication event; prior to their divergence the lineage had a whole genome duplication event. Using SynMap's synonymous mutation overlay, it is easy to determine which syntenic regions are derived from the pre-grass whole genome duplication event or the one specific to maize.
Finding Inversions
- Bacteria Genomic Inversion This example shows an inversion between substrains of Escherichia coli K12, DH10B and W3110.
Ortholog identification and conserved noncoding sequence (CNS) analysis
- Ramosa2 orthologs and CNSs: ramosa2 Encodes a LATERAL ORGAN BOUNDARY Domain Protein That Determines the Fate of Stem Cells in Branch Meristems of Maize [1] Special thanks to Devin O’Connor for writing this tutorial!
- ↑ Esteban Bortiri, George Chuck, Erik Vollbrecht, Torbert Rocheford, Rob Martienssen, and Sarah Hake. 2006 ramosa2 Encodes a LATERAL ORGAN BOUNDARY Domain Protein That Determines the Fate of Stem Cells in Branch Meristems of Maize. Plant Cell 18:574–585
Finding rarely and frequently used codons
- This is very straight forward using OrganismView. Just find your organism and generate a codon usage table.
Videos
OrganismView
OrganismView is CoGe's tool for finding genomes for your organism of interest.
GenomeView
GenomeView is CoGe's interactive genome browser for visualizing genomes, identifying regions of interest, and extracting underlying DNA sequence and genomic features (e.g. genes)
FeatList
FeatList is CoGe's tool for managing lists of genomic features.
SeqView
SeqView is CoGe's tool for generating primary sequence data in fasta format.
