Tutorials: Difference between revisions
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*[[K12 assembly | Bacterial example]] | *[[K12 assembly | Bacterial example]] | ||
*[[Potato version 1 | Plant example]] | *[[Potato version 1 | Plant example]] | ||
===Finding Inversions=== | ===Finding Inversions=== | ||
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===Finding rarely and frequently used codons=== | ===Finding rarely and frequently used codons=== | ||
*This is very straight forward using [[OrganismView]]. Just find your organism and [[generate a codon usage table]]. | *This is very straight forward using [[OrganismView]]. Just find your organism and [[generate a codon usage table]]. | ||
=== Whole 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]] | |||
*[[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. | |||
== Video Tutorials== | == Video Tutorials== | ||
Revision as of 02:08, 30 December 2009
Here you can find tutorials informing you how to get the most out of CoGe's tools.
Original tutorials
You can find a list of CoGe's old tutorials here.
Text Tutorials
What to do with a genome in the early stages of assembly?
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.
Whole 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.
Video Tutorials
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.