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Old 02-16-2013, 01:05 AM   #5
Liam_Gallagher
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Location: Europe

Join Date: Oct 2011
Posts: 18
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Hmm....I would try to use the WT (assembled de-novo) as reference for aligning the mutant and then use a variant caller, to identify variants between two genomes (using the WT as reference).

Also you can take a look at Jspecies. It is a java-based tool that measure the probability if two genomes belonging to the same species or not....and I think you can use your multifasta sequences as input and test your samples for differences. Basically it computes some blast between the samples and for each read you should see the percent of similarity. Then you can investigate the fragments with low similarity....
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