miRNA Target Prediction Based On Sequence

Question

[Tom A]

Hello Biostars,

What are some existing tools/programs that can predict potential miRNA targets based on mature miRNA sequence?

Ideally, I would like to find something contains a built-in 3'UTR alignment of genes and that allows me to input a list of miRNA sequences in a fasta format and a list of gene names (from RefSeq as an example).

Thanks in advance.

Answer 1

[David Langenberger]

You could try TargetSpy. It doesn't even need alignments. That means it can also find species-specific target sites.

[David Langenberger]

There is a stand-alone version on the page under 'downloads'.

[Tom A]

Thanks!