Visual Gene Developer 1.9 – Gene Design software to Analyze, Design, and Optimize Genes

Visual Gene Developer 1.9

:: DESCRIPTION

Visual Gene Developer is a specialized gene design software that has many functions to analyze, design, and optimize genes. Originally, the software was developed to optimize DNA sequence (mainly for codon optimization) of our target genes and has been upgraded to be the general software package since 2008.

::DEVELOPER

Sang-Kyu Jung

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft .Net (dot net) Framework 4.0

:: DOWNLOAD

Visual Gene Developer

:: MORE INFORMATION

Citation

Jung, S.-K. and K. McDonald (2011).
“Visual Gene Developer: a fully programmable bioinformatics software for synthetic gene optimization.”
BMC Bioinformatics 12(1): 340

GenomeMasker 1.3 / GenomeTester 1.3 / SNPmasker 1.1 – Design Unique Genomic PCR Primers

GenomeMasker 1.3 / GenomeTester 1.3 / SNPmasker 1.1

:: DESCRIPTION

The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.

GenomeTester (gtester) is the program that tests 1) whether PCR primers have excessive number of binding sites on template sequence and 2) how many PCR products would be amplified from the template DNA and where are they located.

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GENOMEMASKER

:: MORE INFORMATION

Citation:

Methods Mol Biol. 2015;1275:1-16. doi: 10.1007/978-1-4939-2365-6_1.
Fast masking of repeated primer binding sites in eukaryotic genomes.
Andreson R1, Kaplinski L, Remm M.

Andreson R., Reppo E., Kaplinski L., Remm M.
GENOMEMASKER package for designing unique genomic PCR primers.
BMC Bioinformatics 2006, 7:172.

RNA-Redesign – Web server for Fixed-backbone 3D Design of RNA

RNA-Redesign

:: DESCRIPTION

RNA-Redesign utilizes fixed-backbone design to optimize the primary sequence of a RNA to match a desired backbone, in analogy to fundamental tools that have driven major advances in protein engineering.

::DEVELOPER

RNA-Redesign team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

RNA-Redesign: a web server for fixed-backbone 3D design of RNA.
Yesselman JD, Das R.
Nucleic Acids Res. 2015 May 11. pii: gkv465.

Disperse 1.0.3 – Design of Selector Assays for Targeted Resequencing Applications

Disperse 1.0.3

:: DESCRIPTION

The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes

::DEVELOPER

Disperse Team

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows / Linux
Java
Perl
Blast

:: DOWNLOAD

Disperse

:: MORE INFORMATION

Citation

J. Stenberg, M. Zhang and H. Ji
Disperse–a software system for design of selector probes for exon resequencing applications
Bioinformatics (2009) 25(5): 666-667

NanoTiler 0.11.1 – Design of RNA Nanostructures

NanoTiler 0.11.1

:: DESCRIPTION

NanoTiler is a Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

NanoTiler

:: MORE INFORMATION

Citation:

Methods. 2011 Jun;54(2):239-50. Epub 2010 Dec 14.
Use of RNA structure flexibility data in nanostructure modeling.
Kasprzak W, Bindewald E, Kim TJ, Jaeger L, Shapiro BA.

Cadnano 2.5 – Design Three-dimensional DNA Origami Nanostructures

Cadnano 2.5

:: DESCRIPTION

Cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within Cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.

::DEVELOPER

Cadnano Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX
Autodesk Maya
Python

:: DOWNLOAD

Cadnano

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Aug;37(15):5001-6. Epub 2009 Jun 16.
Rapid prototyping of 3D DNA-origami shapes with caDNAno.
Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM.

FastPCR 6.7.50 – PCR Primers or Probe Design

FastPCR 6.7.50

:: DESCRIPTION

FastPCR software has integrated tools environment that provide comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR) multi-fragments assembling cloning; single primer PCR (design of PCR primers from close located inverted repeat), automatically SSR loci detection and direct PCR primers design, amino acid sequence degenerate PCR, Polymerase Chain Assembly (PCA) or oligos assembly and much more.The “in silico” (virtual) PCR primers or probe searching, comprehensive pairs and individual primers analysis tests are included. The “in silico” oligonucleotide search is helpful for discovering target binding sites with the temperature melting calculation.

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

FastPCR

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1116:271-302. doi: 10.1007/978-1-62703-764-8_18.
FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Kalendar R1, Lee D, Schulman AH.

Kalendar R, Lee D, Schulman AH 2009.
FastPCR Software for PCR Primer and Probe Design and Repeat Search.
Genes, Genomes and Genomics, 3(1): 1-14.

GenoCAD 2.3.1 – Design of Plasmids and Synthetic DNA Sequences

GenoCAD 2.3.1

:: DESCRIPTION

GenoCAD is an open-source computer-assisted-design (CAD) application for synthetic biology. The foundation of GenoCAD is to consider DNA as a language to program synthetic biological systems.

::DEVELOPER

GenoCAD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

GenoCAD

:: MORE INFORMATION

Citation

Writing DNA with GenoCAD.
Czar MJ, Cai Y, Peccoud J.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W40-7. doi: 10.1093/nar/gkp361

DCF 0.6 – Peptide Design by Compatible Functions

DCF 0.6

:: DESCRIPTION

DCF (Design by Compatible Functions) is a peptide design principle for multifunctional peptides based on similarity to a functional reference class.

::DEVELOPER

Christian Diener

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

DCF

:: MORE INFORMATION

Citation

Effective Design of Multifunctional Peptides by Combining Compatible Functions.
Diener C, Garza Ramos Martínez G, Moreno Blas D, Castillo González DA, Corzo G, Castro-Obregon S, Del Rio G.
PLoS Comput Biol. 2016 Apr 20;12(4):e1004786. doi: 10.1371/journal.pcbi.1004786.

CRISPR-DO 0.1 – Genome-wide CRISPR Design and Optimization

CRISPR-DO 0.1

:: DESCRIPTION

CRISPR-DO is a web application for the Design and Optimization of guide sequences in several genomes (human, mouse, fly, worm and zebrafish). CRISPR-DO integrates an sgRNA efficiency prediction model (Xu, et al., 2015) and an off-target scoring function (Hsu, et al., 2013), which allow the users to evaluate the “goodness” of an sgRNA in both sensitivity and specificity.

::DEVELOPER

CRISPR-DO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux /MacOsX
Python

:: DOWNLOAD

CRISPR-DO

:: MORE INFORMATION

Citation:

CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS.
Bioinformatics. 2016 Jul 10. pii: btw476.