Question: Mirna Target Prediction
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gravatar for Gregor Rot
5.2 years ago by
Gregor Rot440
Zurich, Switzerland
Gregor Rot440 wrote:

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

prediction mirna • 1.9k views
ADD COMMENTlink modified 3.6 years ago by Bade40 • written 5.2 years ago by Gregor Rot440
1
  1. There is no 'state of the art' tool
  2. Take a look here: tools for mamalian miRNA target prediction
ADD REPLYlink written 5.2 years ago by Asaf5.5k

Miranda would be of great use.

ADD REPLYlink written 5.2 years ago by ancient_learner610
1
gravatar for lsp03yjh
5.1 years ago by
lsp03yjh750
China
lsp03yjh750 wrote:

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 download page: http://starbase.sysu.edu.cn/download.php

ADD COMMENTlink written 5.1 years ago by lsp03yjh750
0
gravatar for Bade
3.6 years ago by
Bade40
United States
Bade40 wrote:

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 COMMENTlink modified 3.6 years ago • written 3.6 years ago by Bade40
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