We do not have a sequencer so I am using the existing list of miRNAs in miRBase to check if any of these miRNAs are present in the Phytopthora genome. I converted the RNA sequences into DNA to match with the genome. mapper.pl says that there are matches but after running mirdeep2.pl, The output does not give me a single hit. Is the protocol I am following acceptable. What could be the mistake that I am making.
Another problem is for the mature sequence present in the organism file, only one or two miRNAs are currently available for Phytopthora. Also for miRNA from similar sequence, I selected some miRNAs from brown algae which is said to be similar to Phytophthora.
Could somebody give me suggestions.
Another problem is for the mature sequence present in the organism file, only one or two miRNAs are currently available for Phytopthora. Also for miRNA from similar sequence, I selected some miRNAs from brown algae which is said to be similar to Phytophthora.
Could somebody give me suggestions.