There are many miRNA target prediction softwares, can you help me from your experience which one is the best? What are the consideratios I must take? because I have no experience in it perviously.
Thank you so much.
You can search for miRNA targets from various databases, which already exists.There are many prediction databases as well as experimentally validated target databases. MiRDB, miRanda, TargetScan, PITA, Diana-microT-CDS, Microcosm, ma22, EIMMO (Prediction based) and miRTarBAse/miRecords (experimentally validated).
Amarinder Singh Thind
I tried with MiRDB, Thank you
Is there available tool for miRNA- related down stream pathways?
Marwa Hany Do you mean, pathways enrichment from miRNA? I think mirPath v.3 (http://snf-515788.vm.okeanos.grnet.gr/) from Diana tools (http://diana.imis.athena-innovation.gr/DianaTools/index.php) may be helpful for you.
Amarinder Singh Thind Sorry, but what is the most trustedway to get the consensus of results produced by different miRNA target prediction tools?
for example, they predict different memebers of same family for same mi-RNA?
And for one target, if there are 2 different positions that a certain mi-RNA can bind to its target, i just decide on the basis of score and conservation?
Do u know any sources that can help me to understand and interpert the results?
Marwa Hany Article Tools for Sequence-Based miRNA Target Prediction: What to Choose?
take a look on this article if this makes any sense to you. If you are familiar with R. https://github.com/amarinderthind/anamiR/blob/master/R/database_support.R this script will be useful for you to retrieve the consensus of results from various tools (Please take a look on anamiR tool) .- Badges
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