Tutorials

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

How to do phylogenetics with CoGe

• You have a sequence of interest and you want to find homologs of it within and among various genomes in order to do phylogenetic tree reconstructions. CoGe can help. CoGeBlast helps you identify and evaluate homologs from any number of genome, and is linked to FeatList for displaying information about a list of genomic features. FeatList plays a central role in managing lists of genomic features in CoGe and let's you select and send features to other programs in CoGe. One of them is FastaView for generating fasta formatted sequence data. FastaView is linked to phylogeny.fr, and web resource for generating multiple sequence alignments and phylogenetic tree reconstructions. They have a very nice pipeline for automatically generating a decent phylogeny for a set of sequences, and FastaView's link to phylogeny.fr will automatically submit your sequences to their 'one-click' phylogenetic pipeline. Here is the full tutorial: phylogenentics in CoGe

How to download a genome and its annotations

• This is easy using OrganismView. Just search for an organism and genome of interest and use the following links found in the "Genome information" section:

1. "Download sequence in Fasta format" to download the entire genome's DNA sequence in fasta format
2. "Download GFF file" to download all the genomic features in the genome and their annotations in GFF format

How to find syntenic regions between genomes

• This is easy using SynMap to generate syntenic dotplots of whole genome comparisons.

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

• Bacterial example
• Plant example

Finding Inversions

• Bacteria Genomic Inversion E .coli K12 This example shows an inversion between substrains of Escherichia coli K12, DH10B and W3110.
• Bacteria Genomic Inversion Shewanella baltica This example shows an inversion between strains of Shewanella baltica, OS155 and OS185.
• X-alignments: Due to most bacterial inversions occurring symmetrically around the origin of replication, they create "X"-like patterns in syntenic dotplots.

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!

How to find rarely and frequently used codons in a genome

• This is very straight forward using OrganismView. Just find your organism and generate a codon usage table.

How to generate an amino acid usage table for an organism

• This is built into OrganismView and only takes a couple of clicks to generate one. The steps are nearly identical to that for generating a codon usage table.

How to determine the GC content of a genome or chromosome

• This is easy using OrganismView. Just search for an organism and genome of interest and press the link "Click for percent GC content" located next to the length of the genome in the "Genome information" section. For small genomes, this is automatically calculated when the "Genome information" section is loaded.

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.

How to extract all the gene sequences from a genomic region for export from CoGe

• There are times when you want to export sequences from CoGe to another informatics tool. CoGe makes it easy to find the sequences you want and format them for export: How to extract genomic features.

Identifying putative horizontal gene transfer events

• There are several genomic characteristics that can be used to identify genomic regions that are derived from a horizontal gene transfer event. One is the by looking for CDSs that have a different codon usage pattern than neighboring genomic sequence. GenomeView provides a visual way to identify such anomalous genomic regions through one of its genomic visualization layers that colors CDSs based on the GC content of the codon wobble positions: Detecting horizontal gene transfer using GenomeView.

How to find the size of a genome and the genomic features it contains

• Want to know how big a genome is and get a breakdown of the number of genes it contains? Use OrganismView and just search for your organism of interest. It will automatically return these sets of information, and a whole lot more.

How to annotate a genome using CoGe's tools and links to other bioinformatic resources

This tutorial uses CoGe to annotate a Baculovirus genome. Here, CoGe is primarily used to retrieve and organize genomic sequence data, and use its built-in links are used to:

• Build an Excel spreadsheet of all genomic features in a genome including their annotations and sequences.
• Link to NCBI's Blast resource for sequence searching
• Send protein sequences to ProSite for domain identification

The steps outlines here will map to any genome, and works very well for a class project!

Thanks to Dr. Eric Haas-Stapleton for creating this tutorial.

Genomic Web Resources Linking to CoGe

MaizeGDB

MaizeGDB links to CoGe through its genome browser to help researchers find syntenic gene sets between maize and sorghum.

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.

MaizeGDB and CoGe's Maize-Sorghum Orthologies

Researchers can now go directly from MaizeGDB's genome browser to view the same region within CoGe's GenomeView and quickly compared pre-called syntenic orthologous genes between maize and sorghum, as well as the homeologous gene in maize, or when no homeolog was found, the homeologous region in which we would have expected to find it.