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9.6 years ago
The Last Word
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I used the tool psRNATarget to predict the targets of certain miRNAs in a genome of my interest. The targets are however too small to check with BLASTX to find a protein that they might be coding for. If there any bioinformatics methods through which I could annotate the miRNA targets and find what proteins they could be coding for so as to reach a conclusion that a particular miRNA could be influencing the translation of a particular protein.
The seed sequence for miRs are pretty short, only ~7nt so any simple sequence-based search like BLAST will leave you with too many hits, even if you restrict your search to 3' UTRs. Try googling microrna target prediction, there are some databases of in silico predicted targets as well as some that are based on empirical data (Starbase is a good example).