Exons detection - (Aug/10/2005 )
Does any one know how exons in a DNA sequence are detected by hand. That is, some exons are very small, and most gene predictor programs do not detect them, so how were these small exons originally detected. Anyone know how this is done?
I think they were probably found in some cDNA clone.
aligning DNA sequences and mRNA squences.
If using bioinformatics approaches, we can align EST or cDNA sequences to genomic sequences, then in general aligned parts are exons, unalinged are parts are introns.
Problems in these approaches includes:
1. intron retention;
2. composite exons;
3. repetitive sequence elements;
so eventually, there will always be cases that need to be verified by wet-bench approaches. I would assume northern blot with specific targeted probes will work.