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

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.

nondetects 2.16.0 – Model and Impute non-detects in qPCR data

nondetects 2.16.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239

PhiSiGns 1.2 – Indentify Signature Genes in Phages and Design Primers

PhiSiGns 1.2

:: DESCRIPTION

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples. PhiSiGns is intended for phage biologists who want to find common conserved genes in phages for evolution or phylogeny based studies, or who are interested in designing primers that can be used to explore environmental phage diversity.

PhiSiGns Online Version

::DEVELOPER

the Breitbart lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhiSiGns

:: MORE INFORMATION

Citation:

Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, and Mya Breitbart (in review)
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.
BMC Bioinformatics 2012, 13:37

PROBER 2.1 – Fish Oligo Probe Design Software

PROBER 2.1

:: DESCRIPTION

PROBER is an oligonucleotide primer design software application that can generate highly specific probes for use in fluorescence in-situ hybridization (FISH) and other in-situ labeling methods by densely tiling relatively small genomic intervals.  Generating Tiling Oligonucleotide Probes (TOPs) requires software capable of masking repetitive genomic sequences and saturating unique contiguous blocks with small (100-2000bp), DNA probes that will generate a single, strong fluorescent signal for regions as small as a single gene.

::DEVELOPER

Nicholas Navin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • .net framework

:: DOWNLOAD

 PROBER

:: MORE INFORMATION

Citation

Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Maner S, Sebat J, Zetterberg A, Wigler M.
PROBER : oligonucleotide FISH probe design software.
Bioinformatics. 2006 Jun 1. Epub PMID: 16740623

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.

ProbeSpec – Map Specificity of all Candidate Probes for a Given Sequence

ProbeSpec

:: DESCRIPTION

ProbeSpec is a utility for mapping the specificity of all candidate probes for a given sequence (e.g. transcript) against a background containing a large set of sequences (e.g. a transcriptome). Probe specificity is determined by the subsequence in the background that is most similar to its target, the specificity being set as the number of mismatches between the probe and the closest non-specific background sequence.

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ProbeSpec

:: MORE INFORMATION

Citation

Doron Lipson, Peter Web, Zohar Yakhini (2002)
Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome
WABI ’02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics

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.