Mirna Target Prediction

Question

[Gregor Rot]

What is the state-of-the-art tool for miRNA target prediction? I have a FASTA file with sequences and would like to predict miRNA targets in these sequences. Thanks, Gregor

[Asaf]

1. There is no 'state of the art' tool
2. Take a look here: Tools For Mamalian Mirna Target Prediction

[ancient_learner]

Miranda would be of great use.

Answer 1

[lsp03yjh]

Different miRNA target prediction programs produce different results and have high false positive rates. You can use CLIP-Seq datasets to further filter the predicted miRNA targets. starBase collect and curate 111 CLIP-Seq (PAR-CLIP, CLASH, HITS-CLIP, ICLIP) datasets.

You can download them at the download page: http://starbase.sysu.edu.cn/download.php

Answer 2

[Bade]

You didn't mentioned for plants or animals. You can try:

sPARTA for plants - http://nar.oxfordjournals.org/content/42/18/e139

Download Link for sPARTA: https://github.com/atulkakrana/sPARTA.github

miRZA for animals - http://www.nature.com/nmeth/journal/v10/n3/full/nmeth.2341.html

miRZA download requires registration, follow the paper

Bade