Target prediction tool

Question

[vimlakany]

Hi can anyone suggest a good tool for target prediction of sRNA, where batch of sequences can be used as input?

[TriS]

you might need to be more specific about what you want to do, add more details on what you are looking for and what you have in your hands.

Answer 1

[natasha.sernova]

First of all, see Wiki:

https://en.wikipedia.org/wiki/Small_RNA

Known prediction and target-prediction tools:

http://rna.informatik.uni-freiburg.de/CopraRNA/Input.jsp

Bacterial small RNA target prediction software tools

https://omictools.com/bacterial-srna-target-prediction-category

An assessment of bacterial small RNA target prediction programs

http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1020269

sRNAtoolbox: a collection of small RNA analysis tools

http://bioinfo5.ugr.es/srnatoolbox

Review: Predicting sRNAs and Their Targets in Bacteria

http://dx.doi.org.sci-hub.cc/10.1016/j.gpb.2012.09.004#

http://ccb.bmi.ac.cn/starpicker/

and its prediction tool:

http://ccb.bmi.ac.cn/starpicker/prediction.php

ta-si prediction discussion:

http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/ta-si-prediction/

There are a lot of posts on this site about srna, some may be helpful:

Some protocol or pipeline to find sRNA using RNA-seq data in with a reference genome in bacteria

Intergenic region expression

QC and biological repeats of small RNA sequencing data

[vimlakany]

Thank you very much for your reply. All the above tools which you have mentioned doesn't accept batch of input sequences, but I am looking for a tool where batch of sequences (more than 1 sequence) can be given as input to identify targets. Is there any tools available?

[najibveto]

hello you can use http://bioinfo5.ugr.es/srnatoolbox/mirconstarget/ for batch of sequence, or your can download RNA22 or RNAhybrid and use their batch mode in your computer. also same goes for miRanda.