Hi, I want to align cDNA and DNA genomic, but not one vs. one, I have 2 cDNA and 3 genomic sequences, and I would like to see the entire sequence, alignmemt and not alignment, for editing, like clustalx, I tried with clustalx but is not good to do that, I tried with other programs but always in one vs one. The reason if I want to predict a gene, but I only find 3 exons of 7.
Can anyone help me, please?
Well. I have to explain better, please see the image, I've simplified what I want. I have to predict some genes, but in the predicted genes I didnt't find all exones, the reason is that my query genome have several N. If I see the region sequence that did not find exons, may be I can find a little region that are matching. So the program did not find these exons but maybe if I see the sequence I can see these exons.
Note: I tried to use exonerate, augustus, blat and finaly I decided to use the blast for predict genes.
Please see the https://www.dropbox.com/s/dycosy2d5mdj6v9/Predict_genes.png