DNA aligment

Ulrik Ulriks at ruc.dk
Wed Sep 20 10:16:52 EST 2000


Hi all

Does anyone know of software that can align DNA-sequences of different
lenghts?

What I want to do, is to align seuqences of the DNA coding for the same
protein, but from different cells, and see how the promoter regions, exons
and introns differ. I would very much like a number out in the end, telling
how well the different sequences fit

I've been looking around, and it seems that, apart from the number, the
biggest problem is to get the DNA sequences aligned by the transcription
start site and NOT the forst base in the sequence.

Thanks
Ulrik







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