Hello everyone,
I am trying to predict miRNA target sites in long non-coding transcriptome. I have gone through the literature, but most of the algorithms such as TargetScan, miRanda, PicTar are focused on 3'-UTR of coding genes, which is not the case while working with the non coding genes.
Are there any other algorithms/tools which might help me in predicting the miRNA target sites in lincRNAs?
Or is there a way that I can use the above mentioned algorithms by modifying certain parameters?
You may try below tools to predict miRNA target sites in lncRNAs:
i) DIANA-LncBase: http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucl. Acids Res. (2013) 41 (D1)
ii) miRcode: http://www.mircode.org
Respected Sir, thank you very much for your suggestions. I have already gone through the miRcode before.
1) The issues which I had with miRcode is that it uses an older version of GENCODE database as well as the human reference GRCh37. Furthermore, miRcode has not been updated after June 2012.
2)The Gene/transcript type of many of the lincRNAs have been changed to protein coding genes/transcripts in the current version. And since, miRcode has not been updated regularly, this might give rise to some false results.
In my case, I don't want to look for miRNA target sites in the databases. I have some human transcriptome samples with me and I'm interested in predicting miRNA target sites particularly in those samples.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA