Program To Align Cdna And Dna Genomic

Question

[Daniel Fernández]

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?

Thanks

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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

[Michael]

So, this question is about gene prediction, not alignment in general, correct? You got the alpaca genome sequenced, and a gene prediction, but for this highly conserved mammalian gene, you don't get all the exons from your gene predictor you expect, correct? Further, there is no cDNA at all in your set up (e.g. from a full length cDNA sequencing), but you were referring to the predicted transcript (mRNA) sequence which you mistakenly called cDNA, correct?

Answer 1

[Michael]

Did you try these:

• BLAT
• BLAST
• One of the FASTA tools (e.g. SSEARCH)

After trying them all, you can maybe be a bit more specific about what you want to achieve or why they don't do exactly what you want to do.

(And why would you want to do a multiple sequence alignment (clustal-something) of 2 sequences? I guess this is a mistake.)

[Daniel Fernández]

I edit the original post, please see the image

Answer 2

[Vitis]

For this type of tasks, I usually use Sequencher. The bonus is that you can evaluate the quality scores from Sanger traces and take them into account when aligning. If you set a low identity threshold like 70% and 'large gap' to accommodate the introns, the problem in your figure might be solved. The downside is that Sequencher is a commercial software and costs quite a bit, but it's totally worth it if you deal with a lot of Sanger data.