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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:

...

Navigate to the mauve_examples folder that you downloaded and choose:

  • NC_000913.2.gbk - reference genome for a related (but not identical) strain.
  • single.fa
  • pairedc20.fa
  • pairedc25.fa
  • pairedc50.fa

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.gbk
  • single.fa
  • pairedc20.fa
  • pairedc25.fa
  • pairedc50.fa

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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