What strategies can PhD student Daniel Lai use to piece together DNA sequence information for the zebrafish dystrophin gene.
Daniel Lai (PhD student, Auckland University): When you’ve got the dystrophin protein, the peptide sequence, you can take that and go back into the genome and try and figure it [the gene’s nucleotide sequence] out from that. But I’m doing something different. That’s the approach people normally take, but you’ve got the problem that sometimes you’ve got different codons coding for the same peptide.
What people do when they sequence the whole genome is they fragment it. Let’s say with standard sequencing you can do about a thousand base pairs per sequence. Then how are you going to chop up that sequence and guarantee that you can chop it up and get all the fragments you want in the right order? You can’t.
What’s happened at the moment is that because they’re sequencing the whole zebrafish genome, and it’s very incomplete, I’ve got bits back-to-front, upside down, stitched left-right. It’s just horribly stitched together. So I’m taking it, I’m going in, finding what’s there, and then trying to solve it, trying to figure out what’s really meant to be.
You might think, why don’t I just take the mRNA and sequence that and at least have the exon sequence. The problem is that you’ve got to take out all the mRNA and try and fish out the one that could be what you’re looking for.