Tag: Primer

MRPrimerW2 – Search valid Primers for multiple Targets of qPCR experiments without matching Off-targets

MRPrimerW2

:: DESCRIPTION

The MRPrimerW server performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.

::DEVELOPER

Infolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MRPrimerW

:: MORE INFORMATION

Citation

Jeon H, Bae J, Hwang SH, Whang KY, Lee HS, Kim H, Kim MS.
MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.
Nucleic Acids Res. 2019 Jul 2;47(W1):W614-W622. doi: 10.1093/nar/gkz323. PMID: 31045205; PMCID: PMC6602510.

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.
Kim H, Kang N, An K, Koo J, Kim MS.
Nucleic Acids Res. 2016 May 6. pii: gkw380.

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.

HYDEN – A software for Designing Degenerate Primers

HYDEN

:: DESCRIPTION

HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HYDEN

:: MORE INFORMATION

Citation

Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.

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

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

StarPrimer D’Signer 3.0.0.3 – Design of Primers for ENTRY Cloning to Create Donor Vector

StarPrimer D’Signer 3.0.0.3

:: DESCRIPTION

StarPrimer D′Signer is a software to facilitate the design of primers for the ENTRY cloning step to create the Donor Vector. The software is also very well suited for the design of primers in combination with a site-directed mutation approach. In this case it is used to design primers for introducing mutations into your gene of interest which then is transferred into a StarGate ENTRY vector to create a Donor Vector carrying the mutated gene of interest.

::DEVELOPER

IBA GmbH

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Microsoft Silverlight

:: DOWNLOAD

StarPrimer D’Signer

:: 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.

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

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.