I have 100 miRNAs. I want to find their target mRNAs using TargetScan, miRDB. I can search miRNA-mRNA interaction in this tools one by one. Is there a practice way to find 100 miRNA-mRNA interactions in one search using these tools.
Alternatively the ENCORI database (although the site is actaully not responding for me right at this moment) has target predictions for many prediction algorithms, along with experimental evidence from AGO-CLIP experiments available to download as a text file.
You can then use awk, R, pandas, or even excel to filter these files to the miRNAs you are interested in.