Question

Mirna Target Prediction

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10.8 years ago

Gregor Rot ▴ 540

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

mirna prediction • 3.4k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 10.8 years ago by Gregor Rot ▴ 540

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

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 10.8 years ago by Asaf 10k

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Miranda would be of great use.

ADD REPLY • link 10.8 years ago by ancient_learner ▴ 680

Ram · Answer 1 · 2014-03-11

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10.7 years ago

lsp03yjh ▴ 860

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

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 10.7 years ago by lsp03yjh ▴ 860

Ram · Answer 2 · 2015-10-02

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9.2 years ago

Bade ▴ 40

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

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 9.2 years ago by Bade ▴ 40