I have been trying to align my 454 data to a reference sanger sequence in UGENE, but I just can't seem to figure it out. All I want to do is look at intra-individual diversity levels of virions within hosts. Basically, I just need to know what sequences are present, how many there are, how different they are from my original sanger sequence, and the percentage of each sequence within the host.

I think I might have to do an assembly, however every time I try (I've tried both Bowtie and UGENE aligner) it doesn't work. Am I picking the reference sequence wrong? How do I get this to work?? It sounds exactly like what I need.

What I do, is I have my 454 data file in the program. I select it then go to DNA assembly. Then where it asks for the reference sequence, I direct the program to my sanger sequence file. Then I click run without changing any parameters, but it hasn't worked.


Any help is appreciated! Thanks 

Hi, TSchneider I think that should be due to the incompatibility of the data format of the 2 sequences that you wish to align. Raw data from 454 is SFF files whereas Sanger reference is AB1 file. I suspect that should be the reason.

I believe that the option to "Align sequences with a reference file" when first opening my files in UGENE sounds exactly what I need to do. However, whenever I upload my file and click that option-- it doesn't work. Nothing is even uploaded! There is no error message of any kind shown either.