Can anyone help me to identify miRNAs from Assembled Transcriptome (multi fasta contig files around 45,000). I checked with mirBase but it has some limitations. I did a local BLAST using mature miRNA as database there are no hits, it is hitting with stem-loop RNA only. PlantmiRNA database files also do the same only. We have not performed small RNA sequencing. Already we have transcriptome profiles (as contig files). So can you suggest the best online or offline tool for identifying miRNAs and miRNA target prediction tools from Assembled Transcriptome. Thank you
I have not been highly satisfied with the predicted miRNA target annotations, and I think the actual targets are context-dependent (so, only a fraction of targets observed in one experiment may actually be repressed in your own experiment).
However, you can find experimentally defined/validated targets from tarBase:
http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex
You can use RNA-hybrid server
(https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid)
for miRNA Target prediction if you have miRNA sequence and Genes sequence with you.
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