Hi all,
I was wondering.Given the DNA sequence of a protein in bacteria, how can I determine where the signal peptide is in this sequence? I found servers that predict the position of the signal peptides , but they always want the amino acid sequence. What if I need to predict it in the DNA sequence?
Thanks
Is there any way you could translate your sequence into amino acid sequences (e.g.: https://www.ncbi.nlm.nih.gov/orffinder/)? Because, ultimately signal peptide prediction only makes sense when using amino acid sequences (with SignalP being the most widely used one).
Otherwise you could try to predict the gene (in prokaryotes this should actually be easier) on the given DNA string and then find signal peptides. An example of gene finding software is Glimmer: https://ccb.jhu.edu/software/glimmer/
Hope that helps,
Peter
As Peter says, you probably need to translate the DNA sequence into protein. If finding an ORF or a gene is too problematic for whatever reason, I think you could just translate the region of interest blindly in all six frames and search the resulting amino acid sequences. The tool to do that can be found here, for example: http://web.expasy.org/translate/ The output contains stars for stop codons, so you may need to change them to X, depending on the signal peptide prediction software requirements (allowed symbols).
You can try SignalP which is a tool which predicts the signal peptides in a given protein sequence.
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