Tutorials

Here you can find tutorials informing you how to get the most out of CoGe's tools. (Please note that this wiki is new, and we are working on adding information as quickly as we can.)

Original tutorials

You can find a list of CoGe's old tutorials here.

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What to do with a genome in the early stages of assembly?

• Bacterial example
• Plant example

Genome Comparison and Analysis using SynMap and GEvo

• Analysis of differences found between Escherichia coli strain K12 DH10B and strain B REL606 using SynMap and GEvo analysis

In this exercise you will compare the genomes of two Escherichia coli strains, K12 DH10B and B REL606 using SynMap and GEvo analysis. In addition, we will observe the differences between these two genomes as a result of lineage divergence between the two E-coli strain and changes accumulated independently of lineage divergence. The computational tools used to do this analysis can be used for comparing genomes of any species. In two closely related bacterial genomes, for instance, several differences could be found such as transposition, insertions, deletions, duplications, inversion and translocations.

First, we need to construct a syntenic dotplot of K12 DH10B and B REL606 using SynMap. Go to www.synteny.cnr.berkeley.edu/CoGe/Synmap.pl. Search for E-coli K12 strain DH10B and E-coli B strain REL606 in the database of Organism 1 and Organism 2 respectively. Click on "generate synmap". This program will lay the two genomes on the axes and indicate regions of similarities between the two as green dots on a syntenic dotplot. The collection of these dots appear as green line.

In order to accurately account for the "breaks" or discontinuties in the dotplot, we need to run GEvo analysis. GEvo uses multiple algorithms to run comparisons between the two genomic regions. These discontinuties in a dotplot represent the sites of insertions or deletions. More information on GEvo software tool can be found at: .On the dotplot diagram, use the locator to click on the green spot right before a "break". The locator will turn "red" once you have placed it on basepairs/green dots.

After clicking, a new page of GEvo (web add) will appear. Click "Run GEvo Analysis!". This will allow you to visualize and compare the genetic make-up of strain B REL606 and strain K DH10B at a given region. In this case, our region of interest corresponds to a discontunity in our dotplot.

Once GEvo analysis appears, we can begin to look for differences between the two genomes. Click on individual genes/green bars and its annotation will appear in a box.

Repeat the above mentioned steps for each discontinuity in dotplot for individual analysis. The translocation events can be observed from dotplot as well. Notice the fragments of green line all over the dotplot. Place the locator on these and run GEvo to determine which genes were translocated.

Click on the pink bars above a DNA segment and it will connect to its syntenic region. A sliding window can be used to magnify a region we want to analyze. Notice the edges of pink bars connecting syntenic regions. They may run parallel or cross each other. The latter represents an inversion event.

Evidence for deletion and insertions can be located on these genomes using GEvo. At several instants, transposon insertions will account for deletions/insertions in bacterial genomes.

You can also distinguish the segment containing different GC content relative to other parts of genomes. Under GEvo Configuration, click "Results Parameters" and select "Yes" for "Color wobble codon GC content". Click "Run GEvo Analysis!". The region containing different GC content will appear red.

Beware of the

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 Special thanks to Devin O’Connor for writing this tutorial!

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.