Best way to align (multiple, small, near-identical) whole genomes

[OBBARD Darren]

Hi!

I wish to align about 20 whole (but small, 180kbp) virus genomes. I expect them to be very similar at the sequence level, but they may have some rearrangements, and because they're circular they may be circularly permuted (if you see what I mean?)

I'd like a tool that minimises the differences (by selecting the right orientation and starting point for the alignment) and gives me back either a complete alignment or some visualisation of it.

Is there something out there that does this? (I imagine there must be!) and what does it best? (by which I mean easiest to install and use)

Thanks!

D.

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Darren Obbard
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[Sinclair Cooper]

Hi Darren, 

Might be worth dropping Nick Savil/Achim Schnaufer a mail. I worked on something similar for trypanosome minicircles ages ago, I reckon they have some better way of doing it now. 

Cheers, 

Sinclair

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[Bryan Wee]

Hi Darren, 

To interactively visualise bacterial genomes with potential rearrangements, I would use Artemis (which takes blastn -outfmt 6 files as input).  However, it might get a little unwieldy with more than 10 genomes. But if you have a big screen and enough memory you should definitely try. If you find generating blast alignments for each of your sequences a little troublesome, try my script which does the blast for you https://github.com/bawee/bwast and loads it up in Artemis in one command. 

If you just need a simple static figure drawn of 20 alignments I would put the sequences through something like Easyfig, which takes in fasta/ genbank and does the blast for you. There is a command line version of Easyfig so you can run it on 20 genomes in one command. 

Finally, if I had to reorientate circular genomes to a consistent start site I would use the circlator fixstart tool. You just need to tell it what gene to use as the start. 

Hope that helps,

Bryan