Google search and different RNASeq experiments highlights many types of RNA bases for read alignments. Can someone suggest a user friendly base fro small micro RNA alignments to known sequences?
TargetScan is the the most robust tool, because it enables a more complete search at isoform level, it penalizes the less conserved interactions, and its databases are the most up-to-date. For these reasons, TargetScan can predict miRNA:mRNA interactions with a higher probability of being biologically validated than the other tools.
I use UGENE. It is a free software suite with lots of capabilities. You can align your reads to a template all at once and visualize it. It is very easy to do.