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.

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

QDD 3.1.2 / QDD-VM 3.1.2 – Select Microsatellite Markers and Design Primers

QDD 3.1.2 / QDD-VM 3.1.2

:: DESCRIPTION

QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input.

QDD-VM (QDD in a virtual machine) is an easy but greedy installation. The virtual machine (VM) comes with QDD and (almost) all its dependencies installed in a Galaxy server.

::DEVELOPER

Emese Meglécz and Jean-François Martin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 QDD / QDD-VM

:: MORE INFORMATION

Citation

Meglécz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., Martin, J.F. 2010.
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.
Bioinformatics 2010; Vol. 26,3 : 403-404; doi: 10.1093/bioinformatics/btp670.

QUALITY 1.1.6 – Variant of the minimum Chi-squared method for limiting Dilution Assays

QUALITY 1.1.6

:: DESCRIPTION

The program QUALITY is a variant of the minimum Chi-squared (MC) method for limiting dilution assays, and for which he has demonstrated by simulation desirable properties of minimum variance (i.e., high precision) and minimum bias. Our method modifies the MC method to allow the user to specify the probabilities of a false negative and false positive PCR.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

QUALITY

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 QUALITY

:: MORE INFORMATION

Citation

AIDS Res Hum Retroviruses. 1997 Jun 10;13(9):737-42.
Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays.
Rodrigo AG1, Goracke PC, Rowhanian K, Mullins JI.

PolyMarker – Fast Polyploid Primer Design Pipeline

PolyMarker

:: DESCRIPTION

PolyMarker is a tool that simplifies the design of genetic markers, a laboratory test to know if certain variant of the genome is present or not in a plant.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069.

GLAPD – Whole Genome based LAMP Primer Design for a set of Target Genome

GLAPD

:: DESCRIPTION

GLAPD can design LAMPP(Loop-mediated isothermal amplification) primer sets based on a whole genome. It can also design LAMP primers for a set of target genomes. Users can specify a group of background genomes.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Bowtie
  • CUDA driver

:: DOWNLOAD

GLAPD

:: MORE INFORMATION

PrimerZ 20171130 – Streamlined Primer design for Promoters, Exons and Human SNPs

PrimerZ 20171130

:: DESCRIPTION

PrimerZ is a web application dedicated primarily to primer design for genes and human SNPs.

::DEVELOPER

PrimerZ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PrimerZ: streamlined primer design for promoters, exons and human SNPs.
Tsai MF, Lin YJ, Cheng YC, Lee KH, Huang CC, Chen YT, Yao A.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W63-5. Epub 2007 May 30.

SeqState 1.4.1 – Primer Design, Sequence Statistics & Indel Coding

SeqState 1.4.1

:: DESCRIPTION

SeqState is a software for primer design and sequence statistics for phylogenetic DNA data sets.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

SeqState

:: MORE INFORMATION

Citation

Müller K:
SeqState primer design and sequence statistics for phylogenetic DNA data sets
Applied Bioinformatics 2005, 4:65-69

Müller K
Incorporating information from length-mutational events into phylogenetic analysis.
Molecular Phylogenetics and Evolution 2006, 38:667-676

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.