FINDTAR3: Yaou Lab MicroRNA Target Prediction and Analysis

Frequently Asked Question

Q:Can I run FindTar3 program in my local computer?

A:Yes. FindTar3 is a open source program. We provide programs that can directly run on Linux, Windows and Mac OS X as well as source code for advanced users. You can acquire all related package in the download page of this website.

 

Q:Can I download predicted target file?

A:Yes, after you submitted your query miRNA and query mRNA sequence, name or ID number, the server will feedback you the result in a table very soon. At the bottom of this table, there is a button "Download target file", which can save the exactly miRNA targt file you saw in your local computer in the format friendly to miRBrowser. We also supported export to CSV file for target file. However, we highly suggested you to use miRBrowser for browsing and analyzing target files.

 

Q:Why can't I use miRBrowser in Mac OS X?

A:MiRBrowser is a Perl program, it is natively supported by Mac OS X or above. Running of miRBrowser requires Tk module, please make sure your local computer has installed Perl/Tk. You can install it directlyfrom CPAN.

 

Q:Why there are multiple gene 3'UTR choices for a single inputed gene name?

A:The 3'UTR of a specific gene may have different variants, different RefSeq number represent different splicing form of the specific gene. In different cell status or in different organs, gene may express different variants. Therefore, we provided a RefSeq number selection in order to make you easiler to choose exactly what you want, instead of outputting a single (usually the longest) 3'UTR sequence for you.

 

Q:What are the criteria for assessing a target as "excellent", "good" or "ok"?

A:We set up a combinatorial assessing criteria for each target predicted by FindTar3 based on central loop score and free energy, and classified targets as "ok", "good" and "excellent".

ok: i)free energy no greater than -15 kcal/mol, central loop score equal or greater than 10 and less than 15; ii)or absolute value of free energy multiple central loop score no less than 200; iii)free energy equal or less than -30kcal/mol. Targets satisified any of these three condition were recommended as "ok".

good: based on the criteria of "ok", if central loop score higher than 15 and no less than 20, targets were recommended as "good".

excellent: based on the criteria of "ok", if central loop score equal or higher than 20, targets were recommended as "excellent".

 

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