:: DESCRIPTION
OligoFaktory Standalone Edition is a free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more…
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics (2006) 22 (1): 115-116.
OLIGOFAKTORY: a visual tool for interactive oligonucleotide design
Colas Schretter and Michel C. Milinkovitch
:: DESCRIPTION
Mutagenesis Primer Generator is a simple windows GUI program to generate mutagenesis primer by inputting sequence, amino acid number, and letter of amino acid you want to mutate to.
::DEVELOPER
Jonas Lee (jonaslee@berkeley.edu) in Prof. S H Kim’s Lab UC Berkeley
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ProbeMaker is a Java software project aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics 2005, 6:229
ProbeMaker: an extensible framework for design of sets of oligonucleotide probes
Johan Stenberg, Mats Nilsson and Ulf Landegren
:: DESCRIPTION
DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Karl Diedrich
DEODAS: A DEgenerate Oligonucleotide Design and Analysis System
:: DESCRIPTION
mPrimer3 (Modified Primer3) is a modification of Primer3
::DEVELOPER
Department of Bioinformatics, University of Tartu
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 May 15;23(10):1289-91. Epub 2007 Mar 22.
Enhancements and modifications of primer design program Primer3.
Koressaar T, Remm M.
:: 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.
::DEVELOPER
Department of Bioinformatics, University of Tartu
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
SLICSel is a program for designing specific oligonucleotide probes for microbial detection and identification. To obtain maximal specificity of designed oligonucleotides, SLICSel uses the Nearest-Neighbor thermodynamics-based approach for probe design.
::DEVELOPER
Department of Bioinformatics, University of Tartu
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Biotechnol. 2011 Feb 28;11:17.
Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.
Scheler O, Kaplinski L, Glynn B, Palta P, Parkel S, Toome K, Maher M, Barry T, Remm M, Kurg A.
:: DESCRIPTION
HTqPCR, a package for the R statistical computing environment, is a software to enable the processing and analysis of qPCR data across multiple conditions and replicates.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2009 Dec 15;25(24):3325-6. Epub 2009 Oct 6.
HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
Dvinge H, Bertone P.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from quantitative real-time polymerase chain reaction (qPCR) experiments. It comprises a parser to automatically import generated data from qPCR devices and includes a variety of analysis methods to calculate Ct and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporates sample or gene specific efficiency, normalization using single or multiple housekeeping genes, inter-run calibration, and fold change calculation. Moreover, the application supports proper error propagation throughout all analysis steps and allows conducting statistical tests on sample classes. Results can be visualized in highly customizable charts and exported for further investigation.
::DEVELOPER
Genomics & Bioinformatics Graz, Graz University of Technology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pabinger S, Thallinger GG, Snajder R, Eichhorn H, Rader R, Trajanoski Z.
QPCR: Application for real-time PCR data management and analysis.
BMC Bioinformatics 2009, 10:268
