Tag: PCR Primer

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0 – PCR Primer Design Tool

Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0

:: DESCRIPTION

Primer3 is a widely used program for designing PCR primers (PCR = “Polymerase Chain Reaction”). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

Primer3-web is the original web-interface to Primer3.

Primer3Plus is an updated, task-oriented web-interface to Primer3.

::DEVELOPER

developed at Whitehead_Institute and Howard Hughes Medical Institute by Steve Rozen and Helen Skaletsky.

:: SCREENSHOTS

:: REQUIREMENTS

    • Linux / Windows / Mac OsX

:: DOWNLOAD

Primer3

:: MORE INFORMATION

Citation

Steve Rozen and Helen J. Skaletsky (2000)
Primer3 on the WWW for general users and for biologist programmers.
In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386

Oligo Heat Map 1.52 – Check Thermodynamical Parameters for PCR primers

Oligo Heat Map 1.52

:: DESCRIPTION

OligoHeatMap (OHM) is a web-application for checking thermodynamical parameters for PCR primers and computing graphical representation to show specificity of target sequences .

::DEVELOPER

Olivier Croce

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Javascript
  • Php

:: DOWNLOAD

    Oligo Heat Map

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W154-6. Epub 2008 Apr 25.
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.
Croce O, Chevenet F, Christen R.

PrimerProspector 1.0.1 – Design and Analyze PCR Primers

PrimerProspector 1.0.1

:: DESCRIPTION

PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • PyCogent
  • Numpy
  • Matplotlib

:: DOWNLOAD

 PrimerProspector

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087.
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R.

MEDUSA – Selection and Visual Assessment of PCR Primer Pair

MEDUSA

:: DESCRIPTION

MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

 MEDUSA

:: MORE INFORMATION

Citation

Bioinformatics. 2001 Jul;17(7):656-7.
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Podowski RM, Sonnhammer EL.

In-Silico PCR 34 – Searches a Sequence Database with a pair of PCR Primers

In-Silico PCR 34

:: DESCRIPTION

In-Silico PCR searches a sequence database with a pair of PCR primers. It uses an indexing strategy to do this quickly. When the search is successful the output is a fasta format sequence file containing all the regions in the database that lie between the primer pair.

In-Silico PCR Online Version

::DEVELOPER

Jim Kent

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Source Code

:: MORE INFORMATION

PrimerDesigner 1.7 – Design PCR Primers

PrimerDesigner 1.7

:: DESCRIPTION

PrimerDesigner (Primer Design Tool) is a simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them.

::DEVELOPER

Victor Khangulov  vkhangulov@jhu.edu @ BGME lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Python

:: DOWNLOAD

 PrimerDesigner

:: MORE INFORMATION

MultiPLX 2.1 – Analyze PCR Primer Compatibility

MultiPLX 2.1

:: DESCRIPTION

MultiPLX is a tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution. It uses state-of-the-art nearest neighbour DNA binding thermodynamics to estimate possible unwanted pairings between PCR samples.

MultiPLX Online Version

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 MultiPLX

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Apr 15;21(8):1701-2. Epub 2004 Dec 14.
MultiPLX: automatic grouping and evaluation of PCR primers.
Kaplinski L, Andreson R, Puurand T, Remm M.

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