Dear members, I was wondering if anyone can recommend software for aligning endogenous microRNAs (from mirBASE) with a custom mRNA sequence our lab recently received. I looked into the microRNA package, but it only allows for perfect alignment, which I believe is limited to prokaryotes? Thank you in advanced! Jason -- Jason Shoemaker, Ph D Japanese Science and Technology Agency Infection Induced Host Response Laboratory The Institute of Medical Science, University of Tokyo [[alternative HTML version deleted]]