"scale" parameter in MiRanda · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

"scale" parameter in MiRanda

Hello all, I am using MiRanda for performing miR-target predictions on some 3'UTR sequences(hsa). I don't completely understand the "scale" parameter. I guess this parameter inclines to conservation in MiRanda. By default it is 4.0. But how to set this parameter? I mean, how can I get to know the optimum "scale" parameter for my analysis?

rna-seq

• 1,307 views • link

written 7.7 years ago by glady

0 answers

No answers yet.

Log in to answer this question.

More posts like this

miRNA nomenclature and how to handle miRNAs
written 4.5 years ago by bio_elle •

I'm trying to understand how to work with microrna data and I am having some struggles with the nomenclature. If I understood correctly from this …
Using MiRanda for miRNA - PCG interactions
written 7.4 years ago by glady

Hello everyone, I working on some human samples, I have their mRNA and the miRNA dataset in triplicates. Now, I'm interested in studying the miRNA …
score parameter in multimiR
written 7.7 years ago by glady

Hello everyone, Can anyone please guide me about the scoring parameter in multimiR. When you observe the table :View(example5@data). In this table you find a …
how to install & run miRanda
written 9.3 years ago by stijn.vandenbrande •

Hello, I have no experience what so ever regarding bio-informatics. Now, for my research, I would like to do microRNA target predictions using the miRanda …
Miranda Output Parsing
written 10.7 years ago by najibveto •

<p>hello everyone one</p> <p>i am doing microrna prediction target using Miranda. i used the Java based version and i got a long list of hits …
controling miRanda conservation filtering
written 11.5 years ago by dolevrahat •

Hello I am trying to generate an estimate of the number of microRNA targets of several orthlogous miRNAs across a set of animal species. Specifically, …
Seed Search Of Pattern Sequence In A Given Fasta File Database
written 12.6 years ago by Varun Gupta

<p>Hello Everyone</p> <p>I have a fasta file of seed sequences. It looks like this</p> <pre><code>>hsa-miR-140-5p_1_8 AACCACTG >hsa-miR-140-5p_1_7 ACCACTG >hsa-miR-140-5p_1_6 CCACTG >hsa-miR-140-5p_2_8 AACCACT >hsa-miR-140-5p_2_7 ACCACT </code></pre> …
Ensemble Identifier Of Mirna
written 12.8 years ago by khan •

<p>Hi,</p> <p>I have miRNA microarray expression data. I want to do gene set enrichment analysis on this data set. in order to do that, I …
Extraction Of Certain Lines Which Starts And Ends With A Particular Description.
written 13.0 years ago by Abdul Rawoof

<p>Hello everyone,</p> <p>I am trying to extract the lines which starts from ">>" and ends with "Complete" from my Input file.</p> <p><strong>INPUT FILE:</strong></p> <pre><code> Read …
From Microrna Prediction Databases To Microrna / Target Matrices
written 15.4 years ago by Some •

<p>Hi there,</p> <p>There are a lot of different microRNA prediction databases out there. </p> <p>Since people apparently are using those a lot, I am wondering …