Ugene

[Resa7362]

I am trying to align my 454 sequences to reference sanger sequences in order to see the amount of intra-individual virion diversity. I'm working with a virus genome. Does anyone know how to do this in UGENE?? I've been trying to find a program to do this for a while now and I just can't seem to figure it out. I think UGENE will do what I want it to do, but I am not a computer person!

Thanks!

[maubp]

Did you rule out a 454 mapper like Roche's gsMapper from their "Newbler" suite of off instrument applications? That's what I would try first here.

[kga1978]

If you can get somebody to help you out with the computer side (which really is necessary for largeish projects), I would suggest trying out the 454 suite developed by the Broad and just released:

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics-analysis-software?package=RC454

If you just have a couple of samples, you could try out Geneious or CLC Bio - they can both do alignment/assembly as well as intrahost variant calling. I personally use Geneious and like it as a non-command line alternative for small and quick projects.

[Resa7362]

I have been trying different programs for a few months and haven't been able to get anything to do what I've been trying to do. In actuality, it's very very simple. I want to use something that is easy to use since I am not computer savvy. Are these programs user friendly?

[colindaven]

Try, or get someone, to install Roche's Newbler package. It has a nice GUI and is user friendly.

If you want to spend money, CLC is great for 454. A trial version might be the way to go.

Thanks for the tip on the Broad package kga, I'll give it a go sometime.

[kga1978]

Install the trial versions of CLC Genome Workbench and Geneious. They both align 454 data quite well and you can make up your mind of which one you like the most.

Both programs are also user friendly, although you need to have a look at the manual for an hour or so before starting your analyses.