AMUSER 1.0 – Design of Optimal PCR Primers for USER Cloning

AMUSER 1.0

:: DESCRIPTION

AMUSER (Automated DNA Modifications with USER cloning) offers quick and easy design of PCR primers optimized for various USER cloning based DNA engineering

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly.
Genee HJ, Bonde MT, Bagger FO, Jespersen JB, Sommer MO, Wernersson R, Olsen LR.
ACS Synth Biol. 2015 Mar 20;4(3):342-9. doi: 10.1021/sb500194z.

pcrcoal 1.2.0 – Coalescent Simulations of PCR

pcrcoal 1.2.0

:: DESCRIPTION

pcrcoal is an R package implementing the coalescent approach to PCR simulation

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 pcrcoal

:: MORE INFORMATION

Citation:

Weiss, G, von Haeseler, A (1997)
A coalescent approach to the polymerase chain reaction.
NAR 25(15): 3082-3087

PrecisePrimer – Designing PCR Primers for DNA library Cloning and DNA Shuffling

PrecisePrimer

:: DESCRIPTION

PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries.

::DEVELOPER

Jean-Loup Faulon’s group at Micalis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W205-9. doi: 10.1093/nar/gku393. Epub 2014 May 14.
PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.
Pauthenier C, Faulon JL

PCR Analyzer v 1.02 – Estimate for Initial Amount of Amplicon Present in a PCR

PCR Analyzer v 1.02

:: DESCRIPTION

PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.

::DEVELOPER

National Institute of Environmental Health Sciences , National Institute of Health

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCR Analyzer

:: MORE INFORMATION

Citation

Marjo V Smith , Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
BMC Bioinformatics 2007, 8:409doi:10.1186/1471-2105-8-409

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.

MPRIMER – High-throughput Multiplex PCR Primer Design

MPRIMER

:: DESCRIPTION

MPRIMER is a reliable, flexible and high-throughput multiplex PCR primer design software. It i) utilizes the famous Primer3 program to select candidate primers; ii) uses thermodynamics to measure the stability of misprimer and dimers; iii) implements k-mer index algorithm to fast check the specificity against large genome database; iv) designs a flexible plugin mechanism for easily extending the applications; v) has a self-learning system to redesign primers when primers are incompatible; vi) can auto-group the incompatible templates into different tubes; vii) is suitable for high-throughput primer design.

::DEVELOPER

CZlab @ Beijing Institute of Radiation Medcine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang.
MPprimer: a program for reliable multiplex PCR primer design.
BMC Bioinformatics, 2010, 11:143

Primerize 1.0 – PCR Assembly Primer Design

Primerize 1.0

:: DESCRIPTION

Primerize is a Web Server for primer designs of DNA sequence PCR assembly. Primerize is optimized to reduce primer boundaries mispriming, is designed for fixed sequences of RNA problems, and passed wide and stringent tests.

::DEVELOPER

DAS lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 Primerize

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 May 20. pii: gkv538.
Primerize: automated primer assembly for transcribing non-coding RNA domains.
Tian S, Yesselman JD, Cordero P, Das R

PRISE – Designing Sequence-selective PCR Primers

PRISE

:: DESCRIPTION

PRISE (PRImer Selector) is an interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3′ end of the primers – a property that is crucial for sequence selectivity / specificity

::DEVELOPER

Rachid OunitAlgorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

PRISE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PRISE

:: MORE INFORMATION

Citation

J Microbiol Methods. 2008 Mar;72(3):263-7. doi: 10.1016/j.mimet.2007.12.004.
PRISE (PRImer SElector): software for designing sequence-selective PCR primers.
Fu Q1, Ruegger P, Bent E, Chrobak M, Borneman J.

AmplifX 1.7.0 – Manage & Design Primers for PCR

AmplifX 1.7.0

:: 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