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.

HYDEN – A software for Designing Degenerate Primers

HYDEN

:: DESCRIPTION

HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HYDEN

:: MORE INFORMATION

Citation

Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.

PrimerProspector 1.0.1 – Design and Analyze PCR Primers

PrimerProspector 1.0.1

:: DESCRIPTION

PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • PyCogent
  • Numpy
  • Matplotlib

:: DOWNLOAD

 PrimerProspector

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087.
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R.

BOND – Basic OligoNucleotide Design

BOND

:: DESCRIPTION

BOND is a program for designing DNA oligonucleotides. In comprehensive testing, it achieved 100% sensitivity and specificity.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BOND

:: MORE INFORMATION

Citation

BOND: Basic OligoNucleotide Design.
Ilie L, Mohamadi H, Golding GB, Smyth WF.
BMC Bioinformatics. 2013 Feb 27;14:69. doi: 10.1186/1471-2105-14-69.

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.