I have mRNA isoforms sequence of human. I want to predict the miRNA binding site on these mRNA isoforms sequences .
Can anybody give me guidance about the software or databases which can help me in this task?
you can try TargetScan http://www.targetscan.org/vert_50/, microT http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microtv4/index or microT-CDS http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index. In all cases you can download the predicted miRNA sites or submit your gene list query.
since you're interested in isoform level, you could download the predicted miRNA binding sites and look for the ones that specifically overlap with your transcript coordinates. also notice that TargetScan and microT are focused on the 3'UTR of genes, while microT-CDS is analyzing the whole coding sequence.
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