I am interested in looking for evidence of positive selection across domains for a group of genes I am working on. I have collected nucleotide coding sequences for each gene from NCBI. These sequences were translated into amino acids to obtain the domain sequences from the SMART domain website. Are there any programs that can convert the amino acid sequences for the domains back into the corresponding nucleotide sequence using the original nucleotide sequence for the gene as a guide?
Hi Heidi,
the EditSeq program of the Lasergene package allows you to back -translate proteins into degenerate DNA, that can be then searched in your original nucleotide sequence.
If your problem is the identification of the DNA sequence encoding the SMART domain I think that a BLAST approach (tBLASTN) would be fine.
good luck
Massimo
Thanks for your response Massimo! I had tried to use blast to search for the nucleotide sequence of my domain but unfortunately it just returns the nucleotide sequence for the whole gene rather than just for my query. I have also tried some of the back-translation tools online but because of redundancy of the genetic code they do not always give me the correct translation. I haven't heard of Editseq before so I will give that a try and see if it does a better job. It would be great if there was a way to input my original nucleotide sequence as the guide to identify the location of the domain sequence!
I have to agree with Massimo, TBLASTN should do the job. Just use it to blast the amino acid sequence of your domain. If you have the GI of your original DNA sequence, you can restrict the search to the relevant sequence: just check the "Align two or more sequences" box and enter the GI in the "Enter Subject Sequence" box. Once you got your alignment, you can select "GenBank" for the best hit in the "Alignments" section. In the upcoming GenBank view, you will get the DNA sequence only for the aligned part. You might need to get the reverse complement ("Customize View"->"Display Options"->"Show reverse complement") if the hit is on the reverse strand.
Yes, that worked! Thanks so much for your help, I really appreciate it!!!
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