I have an amino acid sequence of my target (KO) and there are different potential ORFs that could be initiated, as predicted by expasy-translate. Is there a way to check the strength of the Kozak consensus sequence to predict the possibility of translation, or to determine the biologically relevant ORF out of the 6 ORFs?
I do think there is, it would mean a blast. Ithink by some peculiarities at NCBI or even a specific one.
Mª Angeles Zorrilla Lopez-Perea Thanks, but BLAST only describes the statistical significance of the alignment made between the query and the database sequences right? do you mean to say if it does not appear in BLAST then it is not probable to be transcribed?
(The one I think is best). There was a particular one with a blast
There are specific databases for kozak sequences. But I do remember a particular one which includes alignments. In the same manner for the primer sequences for PCR you may check the specifities for a primer. (with a sequence alignment)
From blast ncbi you may obtain e value p value specifity... It depends what you are looking for
Hello,
You may try this online tool for predicting Kozak sequences within your CDS. It also ranks them in order of reliability:
Prediction of Translation Initiation ATG (dbcls.jp)
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