Micro RNA (miRNA) are a class of small (22 nucleotide in the mature form) non-coding RNA. They are present in plants and animals and function as transcriptional and post-transcriptional regulators of genes. They bind to a complementary region in the transcribed gene to form doublestanded RNA ...

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What is the meaning of conservation site in miRNA-mRNA pairing context?

I am not biologist and just work in Bioinformatics field. Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs? Example: Each of these duplexes ...
7
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2answers
91 views

Naming convention of miRNAs

I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it nomenclature Based on it, I try to figure out what is hsa-let-7a. As far as I understood, hsa refers to ...
4
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2answers
133 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
2
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1answer
122 views

what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
8
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548 views

How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
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29 views

Periods of Heavy Speciation

I have a set of microRNA ages with corresponding labels suggesting which clade they first emerged from. For instance, for hsa-mir-1, let's say, it would have an age of Eutheria. I have several peaks ...
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1answer
31 views

Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an ...
2
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1answer
117 views

Steps to confirm if predicted miRNA is good or bad

I aligned all miRNAs available to the supercontigs of a particular genome with certain parameters (e value of 0.01 and a word match of atleast 7 as suggested in this paper). I have also isolated the ...
3
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1answer
144 views

mFOLD prediction result interpretation

I am trying to predict the secondary structure of certain predicted pre-miRNAs through mFOLD which is the generally accepted technique for structure prediction in most studies. I am finding it hard to ...
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26 views

Known MicroRNA - Gene Systems?

Have there been any experimentally-verified systems of microRNAs targeting a gene set (e.g., in cancer, perhaps)?
7
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48 views

circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...