Hi, I am interested in prediction of miRNAs gene target using a list of miRNAs sequences and a list of specific human genes. Is anyone aware of a software or a web-tool to do that?
Most of the tools that i found are limited to the use of human miRNAs by code (i.e. hsa-miR-1-5p) while I am interested in using non-human miRNAs sequences from a parasite and scan the human genes to see if they can be a target for these.
Looking forward to receive replies, sincerely
SC
Hi
If I understood correctly, you are looking for a miRNA target prediction tool for parasites. If so, several target prediction tools include worm species, which is parasite too. you can give it a try.
https://www.targetscan.org/worm_52/
https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php
http://www.mirtar2go.org/index.html
https://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html
In this you can apply filter
https://tools4mirs.org/software/target_prediction/
Regards
Saurabh
Hi thanks for the reply. I am dealing with parasitic mirna but I am interesting in finding putative target in the host genome (human) and in order to do that I would like to use a selected list of gene that I have found in an ongoing study of comparative transcriptomic (so not interested in testing all the genome but this subset of genes)
Hi Serena, you can do this with TargetScan (the stand-alone version; https://www.targetscan.org/cgi-bin/targetscan/data_download.vert80.cgi)
The installation is not super straight-forward but once this is done, you will be all set; the tool is super flexible. Good luck!
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