I have an amino acid sequence
- If I run it on NCBI tblastn I get the expected results.
But If I take the same amino acid sequence
- Obtain the nucleotide sequence of it using (https://www.bioinformatics.org/sms2/rev_trans.html)
- and run NCBI blastn, I don't find any results ( No significant similarity found.)
Don't know why this is happening.
You are using two different search algorithms, sure you will get different results.
Maybe you can read the article from Altschul et. al. But I am sure you will not read it or will be able to understand. As > 95 % of the people using BLAST have not read the paper or understood it (I am included too).
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-410. doi:10.1016/S0022-2836(05)80360-2
Nevertheless, do you yourself want to understand the algorithm or why are you doing what you are doing? If you have amino acid, why don't you go for simple BlastP? Generally BlastP is better than BlastN results.*
But for simple understanding, watch this, https://www.youtube.com/watch?v=1l2p_Q7QyB4.
What you actually want to do? Why are you using blast?
I'm using BlastN because I'm looking similar nucleotide sequences to the protein I'm working on.
As I have mentioned earlier
When I run it on tblastn I'm getting results. But when I reverse translate the protein sequence and put it on blastn the results are nil.
Anyway, Thank you for your answer and the article suggestion.
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