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GPU-Mummer (Read 6567 times)

Oct 27^th, 2010 at 3:08pm

Jai Offline
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Addition of Mummer ported to GPU (GPU-mummer) for whole genome alignment and analysis would be an extremely useful tool in Ugene.

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Reply #1 - Oct 28^th, 2010 at 6:38pm

Mikhail Fursov Offline
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Jai wrote on Oct 27^th, 2010 at 3:08pm:

Addition of Mummer ported to GPU (GPU-mummer) for whole genome alignment and analysis would be an extremely useful tool in Ugene.

Ok! We will add it to the our TODO feature list.

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UGENE team

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Reply #2 - Dec 16^th, 2011 at 9:05pm

Alvarenga Offline
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Hi! How is the addition of this feature going? A genome aligner would be a great addition to UGENE!

I found Mugsy, which also uses Nucmer:
http://bioinformatics.oxfordjournals.org/content/27/3/334.full
http://mugsy.sourceforge.net/

Its advantadge is that it's more automated than MUMmer (we just need to run one command) and it has scripts to transform from .delta to .maf and from .maf to .fasta. It's licensed under GPL.

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