Difference between revisions of "Tutorials"
From CoGepedia
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==Text Tutorials== | ==Text Tutorials== | ||
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| + | ===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?=== | ===What to do with a genome in the early stages of assembly?=== | ||
Revision as of 20:58, 29 December 2009
Here you can find tutorials informing you how to get the most out of CoGe's tools.
Contents
- 1 Original tutorials
- 2 Text Tutorials
- 2.1 How to find syntenic regions between genomes?
- 2.2 What to do with a genome in the early stages of assembly?
- 2.3 Finding Inversions
- 2.4 Ortholog identification and conserved noncoding sequence (CNS) analysis
- 2.5 Finding rarely and frequently used codons in a genome
- 2.6 Generating an amino acid usage table for an organism
- 2.7 Whole Genome Comparison and Analysis using SynMap and GEvo
- 3 Video Tutorials
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?
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 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
- 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.
