I used LncTar software to predicting mRNA targets of lncRNAs, which took so much time that I could bear that any longer.
Is there any other shortcut for this performance?
Thank you quite a lot!
Hi Leavy,
Is this a performance issue based question or tool recommendation?
If you are looking to get mRNA targets then you can simply predict based on cis function prediction. You can look for the closest coding genes to lncRNAs in 10kb of upstream and downstream using bedtools and then follow it up with a DAVID enrichment analysis.
However if you would like to use a tool, I think there are no other options but to query the databases,
If you have a small list of lncRNAs, you can use these databases
http://rtools.cbrc.jp/cgi-bin/RNARNA/index.pl
http://starbase.sysu.edu.cn/rbpLncRNA.php
http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex-predicted
https://www.lncrna2target.org/.
Hi, For me prediction tools are new thing and I have some question about: http://rtools.cbrc.jp/cgi-bin/RNARNA/index.pl
Do you have any description about this tool?
I do not know if I should take into consideration the MinEergy or SumEnergy to select proper target for my lncRNA.
Should I take the results with the lowest energy?
Thanks for help!
Hi, For me prediction tools are new thing and I have some question about: http://rtools.cbrc.jp/cgi-bin/RNARNA/index.pl
Do you have any description about this tool?
I do not know if I should take into consideration the MinEergy or SumEnergy to select proper target for my lncRNA.
Should I take the results with the lowest energy?
Thanks for help!
Hello, Tomasz! About the tool found in http://rtools.cbrc.jp/cgi-bin/RNARNA/index.pl, you should consider the following:
- minenergy: The minimum interaction energy among the interactions contained in each pair of RNA sequences, computed by intarna. This score is adequate for short RNA sequences or for cases in which the strongest local interaction is dominant.
- sumenergy: The sum of the local interaction energies that are lower than x kcal/mol. This score is adequate for long RNA sequences such as lncRNAs and mRNAs and for cases in which several strong interactions exist.
The publication about this tool you can find in Article Comprehensive prediction of lncRNA–RNA interactions in human...
:)
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