Hi Everyone,
I am working on finding the DNA sequence of the proteins with specific function.
So far, I got around 5 proteins sequences which show a high similarity (> 96%). I use NCBI to find the DNA sequence of these protein sequences. I found each DNA sequences of each protein, then did alignment. They shows the high similarity (>90%).
However, when I did blastn to search for other DNA sequences sharing the similarity with one DNA sequence I got from above step, no significant similarity was found.
I would think the problem is not because of wrong sequence. It may be I should modify the sequences or change parameters in blastn tool, but I don't know how to do this.
If any one knows, would you mind help me to solve this problem?
I would very appreciate for that.
Best regards,
Dung Pham
The 90% similarity you mention is for amino acids or for nucleotides? You should be able to fetch at least the 5. Are you using the cDNA sequences? Which organism is this? Human?
Hi Albino,
It is 90% similarity for amino acids. I am working on bacteria. It is cDNA. The DNA sequence I got using NCBI gene bank. For example, I know protein A in species X. Based on this protein I could find the corresponding DNA sequence of species using NCBI gene bank.
You suggested that I could fetch at least the 5; Actually I didn't get your point. Could you please explain more?
https://www.ezbiocloud.net/
Try to search on other database like EzBioCloud.
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