1
vote
1answer
19 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
votes
1answer
55 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
votes
1answer
51 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 ...
2
votes
2answers
37 views

RNA secondary structure comparison

Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common ...
4
votes
1answer
47 views

Finding RNA Loops

I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even ...
1
vote
0answers
30 views

Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
5
votes
2answers
166 views

First pass protein structure prediction

I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I ...