I'm trying to figure out which is the best database/tool to determinate what RNA binding proteins could bind my gene of interest, since I found many websites that basically can be used to achieve the same result I was wondering if there is someone that is easier to use and/or more reliable. Thanks in advice! ;)
Softberry provides a whole toolbox for almost any bioinformatical analysis! I made quite good experience with bprom for prediction of bacterial promoters and putative binding sites of regulatory elements.
Maybe you find an appropriate tool of Softberry for your question. Also have a look on the amount of publications that used or cited the tool. Thats a good hint whether the tool is reliable or not!
You could try query RBPDB database to scan your RNA sequence for potential RBPs:http://rbpdb.ccbr.utoronto.ca/index.php
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