miRNA alignment to cDNA data
Hello!
I'd like to align mature miRNAs of one species from miRBase database to transcriptome of closely-related species to find target genes for this miRNAs. Are there any tools that help me align RNA to DNA directly? Or do I need convert RNA into DNA and only then align converted sequences to transcriptome?
1 answer
Alignment to transcripts does not mean that the miRNA controls them, It could be suggestive of its nature (canonical or non-canonical). To predict targets you need to use other algorithms or software (as mirdeep, imir, etc) , and read about miRNA controlling mechanism; read about the "seed sequence".
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