Maximum expected accuracy structural neighbors of an RNA secondary structure

Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure.

 

Source code for RNAborMEA can be downloaded from http://sourceforge.net/projects/rnabormea/ or http://bioinformatics.bc.edu/clotelab/RNAborMEA/

Apps Collections for Synthetic Biology

 

Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization [1]. Here are bio-apps collections for you. Personally Tinkercell and UNAFold are mostly used.

Circuit design and simulation
 Biojade http://web.mit.edu/jagoler/www/biojade/
 Tinkercell http://www.tinkercell.com/Home
 Asmparts http://soft.synth-bio.org/asmparts.html
 ProMoT http://www.mpimagdeburg.mpg.de/projects/promot
 GenoCAD http://www.genocad.org/genocad/
 GEC http://research.microsoft.com/gec
 TABASCO http://openwetware.org/wiki/TABASCO#TabascoSimulator
 Hy3S http://hysss.sourceforge.net/index.shtml
Circuit optimization
 Genetdes http://soft.synth-bio.org/genetdes.html
 RoVerGeNe http://iasi.bu.edu/∼batt/rovergene/rovergene.htm
DNA and RNA design
 Gene Designer https://www.dna20.com/index.php?pageID=220
 GeneDesign http://www.genedesign.org
 UNAFold http://www.bioinfo.rpi.edu/applications/hybrid/download.php
 mfold http://mfold.bioinfo.rpi.edu/download/
 DINAMelt http://dinamelt.bioinfo.rpi.edu/
 Vienna RNA package http://www.tbi.univie.ac.at/∼ivo/RNA/
 Vienna RNA web servers http://rna.tbi.univie.ac.at/
 Zinc Finger Tools http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
Protein design
 Rosetta http://www.rosettacommons.org/main.html
 RAPTOR http://www.bioinformaticssolutions.com/products/raptor/index.php
 HHpred http://toolkit.lmb.uni-muenchen.de/hhpred
 Modeler http://salilab.org/modeller/
 PFP http://dragon.bio.purdue.edu/pfp/
 Autodock 4.2 http://autodock.scripps.edu/
 HEX 5.1 http://webloria.loria.fr/∼ritchied/hex/
Integrated workflows
 SynBioSS http://synbioss.sourceforge.net/
 Clotho http://biocad-server.eecs.berkeley.edu/wiki/index.php/Tools
 Biskit http://biskit.sf.net

 

Suggested pages listing useful bio-apps maybe you will like in synthetic biology research:

  1. WikiGenes Toolbox ( http://www.wikigenes.org/e/art/e/187.html). As a free on-line tutorial edited by people all around the world, WikiGenes has spirits of Linux: open-source, sharing, interest, so is WikiGenes-Synthetic-Biology page. It enables you fast-learn what is synthetic life.
  2. OpenWetWare (http://openwetware.org/wiki/Computational_Tools).
  3. JCVI (http://www.jcvi.org/cms/research/software/#c614). This page is from J. Craig Venter Institute.

 

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[1] Marchisio, M. A., & Stelling, J. (2009). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 20(4), 479-485. Retrieved from http://www.sciencedirect.com/science/article/pii/S0958166909001001

microRNAs quantitative assay with Splinted Ligation

Do you still use Northern Blot to quantitate microRNAs expression? Here I recommend Splinted Ligation Assay[1,2], though this method is an old story (published in 2007).   Detection of miRNAs using splinted ligation. Schematic depiction of the assay process. As described in the text, the assay involves: (1) Labeling of the ligation oligonucleotide; (2) concurrent … Read moremicroRNAs quantitative assay with Splinted Ligation