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
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Gregor Rot
2 answers
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
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
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Miranda would be of great use.