So in short, I did a blastn with standalone blast using all known miRNAs against the EST sequences in a genome (word length 7 and e-value 0.01). Now to confirm one of the next steps would be obtain the pre-miRNA sequence of each hit and do an mFOLD for structural confirmation. Each paper I read always mentions to get a sliding window (of 70 - 100 nt length) but how do you get this sliding window from the BLASTN output.. Do you have to code something yourself or is there an easier way to do it. Thanks.
Answer
DISCLAIMER: I have never worked with miRNAs.
However, from what little I know, the mature miRNA is produced by modifying the pre-miRNA. This means that you should be able to infer the pre-miRNA by mapping your miRNA to the genome using a tool like BLAT. Since you already have an EST which represents a transcribed sequence, you can map your EST back to the genome. You can simplify this by using a tool like exonerate that also models splicing.
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