Difference between revisions of "Tutorials"

Revision as of 12:17, 2 January 2010

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 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 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!

Finding 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.

Generating 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.

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.

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.