NeuroPIpred – Tool to Predict, Design and Scan Insect Neuropeptides

NeuroPIpred

:: DESCRIPTION

NeuroPIpred is an in silico method, which is developed to predict and design insect neuropeptides with better efficacy for controlling pest from infesting various crops.

::DEVELOPER

NeuroPIpred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

NeuroPIpred: a tool to predict, design and scan insect neuropeptides.
Agrawal P, Kumar S, Singh A, Raghava GPS, Singh IK.
Sci Rep. 2019 Mar 26;9(1):5129. doi: 10.1038/s41598-019-41538-x.

antaRNA 2.0.1.2 – Ant Colony Optimized RNA Sequence Design

antaRNA 2.0.1.2

:: DESCRIPTION

antaRNA applies the principle of Ant Colony optimization (ACO) to the problem of inverse folding a RNA structure i.e. finding a suitable sequence, which can fold into that structure.

::DEVELOPER

Bioinformatics Group, Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 antaRNA

:: MORE INFORMATION

Citation

antaRNA – Ant Colony Based RNA Sequence Design.
Robert K, Martin M, Rolf B.
Bioinformatics. 2015 May 27. pii: btv319.

Rosetta 3.11 – Simulation and Design of Protein

Rosetta 3.11

:: DESCRIPTION

ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

::DEVELOPER

Rosetta Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Rosetta

:: MORE INFORMATION

Citation

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovi? Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P (2011)
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
Methods Enzymol 487:545-74

BioNetCAD 1.1 – Design, Simulation and Experimental Validation of Synthetic Biochemical Networks

BioNetCAD 1.1

:: DESCRIPTION

BioNetCAD ,a CellDesigner plug-in, is a computer assisted design tool for synthetic biology.

::DEVELOPER

BioNetCAD team

:: SCREENSHOTS

BioNetCAD

:: REQUIREMENTS

:: DOWNLOAD

 BioNetCAD

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Rialle S1, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F.

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.

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

the IROnBioS Group

:: 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.

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

The GenoFAB, LLC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: 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

FastPCR 6.5.55 – PCR Primers or Probe Design

FastPCR 6.5.55

:: 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.

STAMP 1.1 – Microsatellite Marker Design Extension for the Staden package

STAMP 1.1

:: DESCRIPTION

STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.

::DEVELOPER

Christoph Mayer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Staden

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

Array Designer 4.43 – Oligo & cDNA Microarray Design Software

Array Designer 4.43

:: DESCRIPTION

Array Designer designs thousands of primers and probes for oligo and cDNA microarrays in seconds. It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

Array Designer Demo

:: MORE INFORMATION