Tag: Design

NUPACK – Analysis and Design of Nucleic Acid Systems

NUPACK

:: DESCRIPTION

NUPACK is a growing software suite for the analysis and design of nucleic acid systems.NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

::DEVELOPER

NUPACK Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NUPACK

:: MORE INFORMATION

Citation:

.N. Zadeh, C.D. Steenberg, J.S. Bois, B.R. Wolfe, M.B. Pierce, A.R. Khan, R.M. Dirks, N.A. Pierce.
NUPACK: analysis and design of nucleic acid systems.
J Comput Chem, 32, 170–173, 2011.

ORFprimer 1.6.4.1 – High Throughput PCR Primer Design

ORFprimer 1.6.4.1

:: DESCRIPTION

ORFprimer is an extended software package for high throughput PCR primer design for biological sequences.ORFprimer can be used to compute primers for up to thousands of target sequences.This procedure can be automated furthermore by reading the targets through text files.

::DEVELOPER

Konrad Büssow and Steve Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ORFprimer

:: MORE INFORMATION

RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure

RNA-DV 1.0

:: DESCRIPTION

RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).

::DEVELOPER

Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNA-DV

:: MORE INFORMATION

BRD 4.0 – Bioreactor Design

BRD 4.0

:: DESCRIPTION

BRD (Bioreactor Design) is a software to design different kinds of bioreactors. Therefore are three different parts available in the application. In the upper left part, the parameters can be found. In the upper right part the designed bioreactor is shown. In de lower part is a spreadsheet section where the results of the calculations are shown.

::DEVELOPER

Pieter van Santen

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

BRD

:: MORE INFORMATION

Buy now

DNA-CHIP CAD – DNA Array Design

DNA-CHIP CAD

:: DESCRIPTION

DNA-CHIP CAD is a CAD tool for physical design of DNA arrays. Besides using simple academic input and output format, the tool also accepts input files from Affymetrix and outputs their layout format.

::DEVELOPER

Andrew Kahng, Sherief Reda

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DNA-CHIP CAD

:: MORE INFORMATION

Citation:

A. B. Kahng, I. I. Mandoiu, S. Reda, X. Xu, and A. Zelikovsky,
Computer-Aided Optimization of DNA Array Design and Manufacturing
IEEE Transactions on Computer-Aided Design 25 (2) (2006) 305-320.

Exit mobile version