Tag: PCR

FastPCR 6.7.50 – PCR Primers or Probe Design

FastPCR 6.7.50

:: 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.

MFEprimer 3.2.1 – PCR Primer Specificity Checking Program

MFEprimer 3.2.1

:: DESCRIPTION

MFEprimer : Multiple factor evaluation of the specificity of PCR primers. This program is designed to evaluate the specificity of PCR primers based on known multiple factors including sequence similarity, stability at the 3’end of the primer, melting temperature, GC content, and number of binding sites between the primers and DNA templates. It can help the user to select more suitable primers before running either standard or multiplex PCR reactions.

::DEVELOPER

Wubin Qu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MFEprimer

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W205-8. doi: 10.1093/nar/gks552. Epub 2012 Jun 11.
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.
Qu W1, Zhou Y, Zhang Y, Lu Y, Wang X, Zhao D, Yang Y, Zhang C.

Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang and Chenggang Zhang. (2009)
MFEprimer: multiple factor evaluation of the specificity of PCR primers,
Bioinformatics, 25(2), 276-278.

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

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

DesignPrimer – Design PCR Primer Pairs for the SciRoKo output using Primer3

DesignPrimer

:: DESCRIPTION

The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output using Primer3. An output file is generated that can be directly sent to a company for primer synthesis.

::DEVELOPER

Robert Kofler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Perl

:: DOWNLOAD

 DesignPrimer

:: MORE INFORMATION

jPCR 1.15.8 – Java Tools for PCR, in silico PCR, Oligonucleotide Assembly & Analysis

jPCR 1.15.8

:: DESCRIPTION

jPCR is a java application based on FastPCR software and provides comprehensive and professional facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, unique, group-specific, bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR); and microarray design;

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

jPCR

:: 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).

PrimerMatch – PCR Primer Alignment Tools

PrimerMatch

:: DESCRIPTION

The Primer Match suite of tools is designed to find and count exact and near exact matches of short oligonucleotide sequences in large genomic databases. All matches to the oligos will be output, the tools guarantee a complete enumeration of all matches consistent with the search options. Substitutions, insertions and deletions can be prohibited in the start, end, 5′ or 3′ bases of oligos. Many options for constraining acceptable alignments and input/output formats are provided. The tools automatically optimize the sequence search strategies to match the search parameters.

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PrimerMatch

:: MORE INFORMATION

Amplicon b09 – Software for Designing PCR Primers on Aligned DNA Sequences

Amplicon b09

:: DESCRIPTION

 Amplicon is a tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form. This is especially useful for designing ‘group-specific’ PCR primer sets that produce amplicons from a targer group of species, but not from other groups of species. Amplicon assists in group-specific PCR primer desing primarily by being a visualisation tool for alignments from which the user can select regions that may be group-specific primer binding sites. Other useful features that are not common in other PCR primer design software are handling of gapped sequences and degenerate sites in aligned DNA. Group-specific PCR primer sets are useful in a wide variety of situation where environmental DNA is being examined and the diversity or identity of some of the DNA sequences within a sample need to be determined.

::DEVELOPER

Dr Simon Jarman

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Amplicon 

:: MORE INFORMATION

Citation

Jarman SN (2004)
Amplicon: software for designing PCR primers on aligned DNA sequences.
Bioinformatics 20: 1644-1645.