Category: PCR / Primer Design

Primer Prim’er 5.6.0 – PCR Primer Design Tool

Primer Prim’er 5.6.0

:: DESCRIPTION

Primer Prim’er is a PCR primer design tool that completely automates the primer design process.The software generates vector specific PCR primer sets designed to amplify and insert DNA targets into your labs vectors. Primer prim’er is designed to be a powerful tool for structural genomic efforts as well as a teaching tool. Primer prim’er very customizable. Aside from being able to define and employ your own vectors, a variety of settings can be tailored to your needs.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Flash

:: DOWNLOAD

Primer Prim’er

:: MORE INFORMATION

The previously released PERL-CGI version can be found here.

ORFprimer 1.6.4.1 – High Throughput PCR Primer Design

ORFprimer 1.6.4.1

:: DESCRIPTION

ORFprimer is an extended software package for high throughput PCR primer design for biological sequences.ORFprimer can be used to compute primers for up to thousands of target sequences.This procedure can be automated furthermore by reading the targets through text files.

::DEVELOPER

Konrad Büssow and Steve Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ORFprimer

:: MORE INFORMATION

PCRsetup – Tool for Planning PCR and qPCR Reactions

PCRsetup

:: DESCRIPTION

PCRsetup is a tool for planning PCR and qPCR reactions, mixing solutions. The higher quality of primers is help to save PCR efficiency at changing PCR conditions. PCR reaction can set up in room temperature and performed without hot-start enzymes.

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCRsetup

:: MORE INFORMATION

Citation

Kalendar R, Lee D, Schulman AH 2011.
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Genomics, 97(7).

NetPrimer – Free Primer Analysis Software

NetPrimer

:: DESCRIPTION

NetPrimer combines the latest primer design algorithms with a web-based interface allowing the user to analyze primers over the Internet. All primers are analyzed for melting temperature using the nearest neighbor thermodynamic theory to ensure accurate Tm prediction. Primers are analyzed for all secondary structures including hairpins, self-dimers, and cross-dimers in primer pairs. This ensures the availability of the primer for the reaction as well as minimizing the formation of primer dimer. The program eases quantitation of primers by calculating primer molecular weight and optical activity. To facilitate the selection of an optimal primer, each primer is given a rating based on the stability of its secondary structures. A comprehensive analysis report can be printed for individual primers or primer pairs.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

NetPrimer

:: MORE INFORMATION

MeltCalc 2.0 – Thermodynamic Probe Design

MeltCalc 2.0

:: DESCRIPTION

MeltCalc is the ultimate thermodynamic modelling spreadsheet for Excel. The software will provide you with a thermodynamically optimized probe at its best!

::DEVELOPER

Ekkehard Schütz and Nicolas von Ahsen.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Excel

:: DOWNLOAD

MeltCalc

:: MORE INFORMATION

Citation

Ekkehard Schütz and Nicolas von Ahsen.
Influencing factors of dsDNA dye (high-resolution) melting curves and improved genotype call based on thermodynamic considerations
BioTechniques 1999;27:1218

BUY LICENSE

PrimerHunter 1.0.2 – Primer Design for PCR-Based Virus Subtype Identification

PrimerHunter 1.0.2

:: DESCRIPTION

PrimerHunter is a tool for selecting highly sensitive and specific primers for virus subtyping. It takes as input sets of both target and non-target sequences and ensures that selected primers amplify all target sequences and none of the non-target sequences by relying on accurate melting temperature computations based on the nearest-neighbor model of Santalucia and the fractional programming algorithm of  Leber et al.

PrimerHunter Online version

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PrimerHunter

:: MORE INFORMATION

Citation:

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson,
PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification,
Nucleic Acids Research 37, pp. 2483-2492, 2009

G-POT 1.0 / PRIMER-ILP 1.0 – Multiplex-PCR Primer Set Selection

G-POT 1.0 / PRIMER-ILP 1.0

:: DESCRIPTION

G-POT is a primer set selection tool that minimizes the number of primers needed to amplify a set of loci while ensuring that each locus is amplified by a pair of primers located within L basepairs of each other, where L is an input parameter.

PRIMER-ILP is a primer set selection tool that minimizes the number of primers needed to amplify a set of loci while ensuring that each locus is amplified by a pair of primers located within L basepairs of each other, where L is an input parameter. The code uses the mixed integer linear programming solver from the GNU Linear Programming Package (GLPK) to solve the IP problem created from the input target sequences.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

G-POT ; PRIMER-ILP

:: MORE INFORMATION

Citation:

K.M. Konwar, I.I. Mandoiu, A.C. Russell, and A.A. Shvartsman.
Improved Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints,
Proc. 3rd Asia-Pacific Bioinformatics Conference (APBC), pp. 41-50, 2005.

DNA-BAR – Select DNA Probes

DNA-BAR

:: DESCRIPTION

DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.

DNA-BAR Online Version

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DNA-BAR

:: MORE INFORMATION

Citation:

B. DasGupta and K.M. Konwar and I.I. Mandoiu and A.A. Shvartsman,
DNA-BAR: Distinguisher Selection for DNA Barcoding,
Bioinformatics 21, pp. 3424-3426, 2005,

JCVI Primer Designer 20101122 – High Throughput PCR Primer Design

JCVI Primer Designer 20101122

:: DESCRIPTION

JCVI Primer Designer is the high throughput PCR primer design software that is used at the J. Craig Venter Institute.

::DEVELOPER

the J. Craig Venter Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

JCVI Primer Designer

:: MORE INFORMATION

Citation

Li K, et al. “Novel computational methods for increasing PCR primer design effectiveness in directed sequencing“. BMC Bioinformatics 2008, 9:191.