Tag: Design

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0 – PCR Primer Design Tool

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0

:: DESCRIPTION

Primer3 is a widely used program for designing PCR primers (PCR = “Polymerase Chain Reaction”). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

Primer3-web is the original web-interface to Primer3.

Primer3Plus is an updated, task-oriented web-interface to Primer3.

::DEVELOPER

developed at Whitehead_Institute and Howard Hughes Medical Institute by Steve Rozen and Helen Skaletsky.

:: SCREENSHOTS

:: REQUIREMENTS

    • Linux / Windows / Mac OsX

:: DOWNLOAD

Primer3

:: MORE INFORMATION

Citation

Steve Rozen and Helen J. Skaletsky (2000)
Primer3 on the WWW for general users and for biologist programmers.
In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386

SynTReN 1.2 – Generator of Synthetic Gene Expression data for Design and Analysis of Structure Learning algorithms

SynTReN 1.2

:: DESCRIPTION

Syntren  (Synthetic Transcriptional Regulatory Networks) is a network generator that creates synthetic transcriptional regulatory networks and produces simulated gene expression data that approximates experimental data. Network topologies are generated by selecting subnetworks from previously described regulatory networks. Interaction kinetics are modeled by equations based on Michaelis-Menten and Hill kinetics. Our results show that the statistical properties of these topologies more closely approximate those of genuine biological networks than do those of different types of random graph models. Several user-definable parameters adjust the complexity of the resulting data set with respect to the structure learning algorithms.

::DEVELOPER

Kathleen Marchal 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

  Syntren

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jan 26;7:43.
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms.
Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, Verschoren A, De Moor B, Marchal K.

AutoGrow 4.0.3 – Use AutoDock Vina in Protein Inhibitor Design

AutoGrow 4.0.3

:: DESCRIPTION

AutoGrow (Java DOCK), uses fragment-based growing, docking, and evolutionary techniques.Due in part to the increasing availability of crystallographic protein structures as well as rapid improvements in computer power, the past few decades have seen an explosion in the field of computer-based rational drug design. Several algorithms have been developed to identify or generate potential ligands in silico by optimizing the ligand-receptor hydrogen bond, electrostatic, and hydrophobic interactions.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AutoGrow

:: MORE INFORMATION

Citation

J Mol Graph Model, 44, 104-12 Jul 2013
AutoGrow 3.0: An Improved Algorithm for Chemically Tractable, Semi-Automated Protein Inhibitor Design
Jacob D Durrant , Steffen Lindert, J Andrew McCammon

Durrant, J. D.; Amaro, R. E.; McCammon, J. A. 2009.
AutoGrow: A Novel Algorithm for Protein Inhibitor Design
Chemical Biology & Drug Design. 73(2):168-78.

PrimeDesign 0.2 – Flexible Design of pegRNAs and ngRNAs for Prime Editing

PrimeDesign 0.2

:: DESCRIPTION

PrimeDesign is a software tool for the flexible and comprehensive design of prime editing. PrimeDesign is an edit-centric design tool for the installation of substitution, insertion, and deletion edits, and is generalizable for both single and combinatorial edits. Taking a single input that encodes both the reference and edit sequence, PrimeDesign enumerates all possible pegRNA protospacers, pegRNA extensions, and ngRNAs within set parameter ranges to install the desired edit(s).

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • Docker

:: DOWNLOAD

PrimeDesign

:: MORE INFORMATION

Citation

Hsu JY, Grünewald J, Szalay R, Shih J, Anzalone AV, Lam KC, Shen MW, Petri K, Liu DR, Joung JK, Pinello L.
PrimeDesign software for rapid and simplified design of prime editing guide RNAs.
Nat Commun. 2021 Feb 15;12(1):1034. doi: 10.1038/s41467-021-21337-7. PMID: 33589617; PMCID: PMC7884779.

GEDpm-cg – Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

GEDpm-cg

:: DESCRIPTION

GEDpm-cg enables users to perform the efficient, automated and high-throughput design of single nucleotide editing in C. glutamicum chromosome. The counter-selection HR system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for genetic modification, vector DNA assembly and sequencing verification were provided as design results.

::DEVELOPER

Biodesign Centre, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

GEDpm-cg

:: MORE INFORMATION

Citation

Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, Luo J, Wang M, Liao X, Ma H.
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum.
Front Bioeng Biotechnol. 2021 Oct 15;9:768289. doi: 10.3389/fbioe.2021.768289. PMID: 34722482; PMCID: PMC8554027.

FindPath – in silico Design of Synthetic Metabolic Pathways

FindPath

:: DESCRIPTION

FindPath is an unified system predicting and ranking the possible pathways according to their metabolic efficiency in cellular context. This tool rely on chemical reactions database to generate all possible metabolic pathways and exploits constraint-based models (CBMs) to identify the synthetic pathway that is the most effective for achieving a desired metabolic function in a given host microorganism.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • MatLab

:: DOWNLOAD

 FindPath

:: MORE INFORMATION

Citation

FindPath: A Matlab solution for in silico design of synthetic metabolic pathways.
Gilles V, Marc C, Jean-Charles P, Stéphanie H.
Bioinformatics. 2014 Jul 3. pii: btu422.

D-Tailor 20130924 – Automated Analysis and Design of DNA Sequences

D-Tailor 20130924

:: DESCRIPTION

D-Tailor (DNA-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of sequence analysis tools into a Monte-Carlo algorithm that evolves synthetic sequences towards user-defined goals.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Python

:: DOWNLOAD

 D-Tailor

:: MORE INFORMATION

Bioinformatics. 2014 Jan 13.
D-Tailor: automated analysis and design of DNA sequences.
Guimaraes JC1, Rocha M, Arkin AP, Cambray G.

AmplifX 2.1.1 – Manage & Design Primers for PCR

AmplifX 2.1.1

:: DESCRIPTION

AmplifX is a software to search through a collection of primers, such as any molecular biologist has in his refrigerators, to find those which can be use to amplify a fragment into a target sequence, for example, and particularly, to design strategies to screen recombinant clones by PCR. Some information is associated with each primer; some automaticelly computed by AmplifX (like TM, Quality, length) and others given by the user (name, comments,…) This allows general aspects of primer management (sequences and real tubes). AmplifX can also design new primers.

::DEVELOPER

Nicolas Jullien

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX / Linux

:: DOWNLOAD

 AmplifX

:: MORE INFORMATION

Rosetta 3.13 – Simulation and Design of Protein

Rosetta 3.13

:: 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

minRect 1.0.2.1 – Metabolic Network Pathway Design tool on a Boolean model

minRect 1.0.2.1

:: DESCRIPTION

minRect is a new metabolic network pathway design tool on a Boolean model for finding the minimum number of reactions from a reference network, so that the target compound becomes producible in the host network.

::DEVELOPER

Takeyuki Tamura

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++
  • GNU Make
  • CPLEX

:: DOWNLOAD

 minRect

:: MORE INFORMATION

Citation:

Wei Lu,Takeyuki Tamura,Jiangning Song and Tatsuya Akutsu,
“An Integer Programming-based method of designing synthetic metabolic networks by Minimum Reaction Insertion”
PLoS One. 2014 Mar 20;9(3):e92637. doi: 10.1371/journal.pone.0092637. eCollection 2014.