RNAhybrid generatign same p-values for all predicted targets when using exterme value distribution parametres calcaulted by RNAcalibrate
0
0
Entering edit mode
9.3 years ago
dolevrahat ▴ 30

Hello

I am attempting to use RNAcalibrate in order to predict extreme value distribution for some miRNA-target interactions which I intend to then pass to RNAhybrid. As a test I started with the c.elegans miRNA cel-let-7-3p and used dinculotide frequency data I obtained using a R script that analyzed the annotated c.elegans 3'UTR available from ensembl.

However, when I passed the parameters I obtained from RNAcalibrate to RNAhybrid (again querying cel-let-7-3p against all c.elegans 3'UTR), RNAhybrid generated an output in which all predicted targets have a p-value of 1.000. When I tried to run RNAhybrid with the same query and target sequence using RNAhybrid built-in c.elegans 3'UTR set, I did receive different p-values for different targets, indicating that the first output I received was not an artifact of the particular miRNA or target sequences.

When I tried running RNAhybrid against other sets of query and target sequences from other species with evd parameters I obtained using RNAcalibrate I got similar results (that is, all targets had the same p-value, although not necessarily 1.000).

As I indicated, I'm aware of the fact that RNAhybrid has a built-in evd for c.elegans, but I'm working in a project in which I need to generate miRNA target prediction for several species, some of which do not have built in target datasets in RNAhybrid. I started with c.elegans as a test in order to be able to compare the results I get using the evd calculated by RNAcalibrate with the result generated by the built-in target set.

Do you have any idea what the source of the error might be and how I can refine my usage of RNAcalibrate to get more meaningful results? Any help will be highly appreciated.

The command lines I used are provided below if you want to examine them.

Thanks in advance

Dolev Rahat

Command lines:

RNAcalibrate -d celegans_3UTRS.freq -q cel-let-7-5p.fa > cel_let7_evd.txt
RNAhybrid -e -20 -d 1.661933 0.108887 -t celegans_3UTRS.fa -q cel-let-7-5p.fa > RNAhybrid_cel_let_7p_calib.txt
RNAhybrid RNAcalibrate miRNA target-prediction • 3.8k views
ADD COMMENT
0
Entering edit mode

I also get p-value around 0.99 and 1.00 for each . Idont know whether it is acceptable or not? what should i do now???

ADD REPLY

Login before adding your answer.

Traffic: 2536 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6