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In a terminal on your Desktop (local) machine.
| Code Block |
|---|
scp -r username@taccusername@lonestar.tacc.utexas.edu:/corral-repl/utexas/BioITeam/ngs_course/mauve_examples ~/Desktop |
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First we're just going to view two related species versus one another.
Choose: File → Align with progressiveMauve...
Navigate to the mauve_examples folder that you downloaded and choose:
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Navigate to the mauve_examples folder that you downloaded and choose:
NC_000913.2.gbk- reference genome for a related (but not identical) strain.pairedc20.fa
Be sure to add them in this order! We need the reference first.
To remind you of what we are looking at:
| Set 1 | Set 2 | Set 3 | Set 4 |
|---|---|---|---|---|
File Name | single.fa | pairedc50.fa | pairedc25.fa | pairedc20.fa |
Read Size | 100 | 100 | 100 | 100 |
Paired/Single Reads | Single | Paired | Paired | Paired |
Gap Sizes | NA | 400 | 400, 3000 | 400, 3000, 1500 |
Coverage | 50 | 50 | 25 for each subset | 20 for each subset |
Number of Subsets | 1 | 1 | 2 | 3 |
Try out some of the other files as well.
You can also try to assemble all five files at once with Align with progressiveMauve...:
NC_000913.2.gbksingle.fapairedc20.fapairedc25.fapairedc50.fa
Warning! single.fa has a lot of sequences. If you add it to the mix, things will get ugly.
Transferring annotation
Mauve has a useful feature to transfer the coordinates of genes across the alignment that it has made by Move Contigs. This can be a good way of assigning orthologs.
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- Circos - fully featured. Very cool functions for drawing connections between different chromosome locations.
- CGView Simpler to use. Better functionality for showing genes up close as arrows. Does not draw links.
Evaluating eukaryotic assemblies
If you are going to seriously annotate a eukaryotic genome, then you are going to need a machine with database infrastructure and other tools installed. Here are two systems for annotating gene structure in eukaryotic genomes as examples:
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