Pythia 1.0.1
:: DESCRIPTION
Pythia designs PCR primers from a thermodynamic point of view.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows with Cygwin
- Python
:: DOWNLOAD
:: MORE INFORMATION
Tag: PCR
PerlPrimer 1.1.21 – Open-source PCR Primer Design
PerlPrimer 1.1.21
:: DESCRIPTION
PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.
::DEVELOPER
Owen Marshall at Murdoch Childrens Research Institute
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / Linux / MacOSX
- Perl
- Perl/Tk
- libwww-perl-5.76
:: DOWNLOAD
:: MORE INFORMATION
Citation
Owen J. Marshall
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Bioinformatics (2004) 20 (15): 2471-2472.
Sequence Extractor 1.1 – Generates Restriction Map and PCR Primer Map
Sequence Extractor 1.1
:: DESCRIPTION
Sequence Extractor generates a clickable restriction map and PCR primer map of a DNA sequence. Protein translations and intron/exon boundaries are also shown. Use Sequence Extractor to build DNA constructs in silico.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / Linux / Mac OsX
- Perl
:: DOWNLOAD
:: MORE INFORMATION
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
:: 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
- Windows / Linux / MacOSX
- Java
- MySQL / Oracle / Micosoft Access
:: DOWNLOAD
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / Linux / MacOSX
- Java
:: DOWNLOAD
:: 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).
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.
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: 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
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
:: MORE INFORMATION
Citation
Li K, et al. “Novel computational methods for increasing PCR primer design effectiveness in directed sequencing“. BMC Bioinformatics 2008, 9:191.