Hi all!! I would like to do something very simple. I got 6 sequencing results and they are quite long. I would like to compare these sequences with genomic DNA because that is from where I cloned them.
I'm doing it with the align short sequences tools and options by default. Some sequences don't even load, maybe because they have to many mismatches...
Is this the best way to do this??

My best, jose.

Hi! Are you talking about Sanger reads?


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I'm doing it with the align short sequences tools and options by default

Short reads are next-generation sequencing data. There are usually thousand or even millions of them to be aligned. So this is not the right choice for your type of data.


Quote:

Is this the best way to do this??

It is better open the sequences in the Alignment Editor. As you have a reference sequence, add it also to the sequence alignment. Then, you can do pairwise alignment of each sequence with the reference. And also do some additional manual aligning.

If you like, I can show you the procedure in more details in a webinar.

Note, that we're going to improve this procedure in UGENE 1.16.

Note that a new workflow for Sanger reads quality control and alignment has been added in the new UGENE 1.16 version:
https://ugene.unipro.ru/wiki/display/WDD16/Trim+and+Align+Sanger+Reads
https://ugene.unipro.ru/wiki/display/WDD16/How+to+Use+Sample+Workflows

Further improvements in this direction are planned for UGENE 1.17.