:: 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…
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:: 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
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.
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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.
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:: DOWNLOAD
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Citation
Karl Diedrich
DEODAS: A DEgenerate Oligonucleotide Design and Analysis System
:: 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
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.
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:: DESCRIPTION
ProteinCCD use to design truncation constructs of a protein under investigation.
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Structural Biology group of A. Perrakis
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:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W402-5. Epub 2009 Apr 24.
ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments.
Mooij WT, Mitsiki E, Perrakis A.
:: DESCRIPTION
Assembly PCR Oligo Maker is created to automate the design of oligodeoxynucleotides for the PCR based construction of long DNA molecules. This application is designed specifically to aid in the design of DNA molecules that are to be used for the production of RNA molecules by in vitro synthesis with T7 RNA polymerase.
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rydzanicz, R., Zhao, X. S., Johnson, P.E., (2005)
Assembly PCR Oligo Maker: A tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production.
Nucleic Acids Res., 33: W521-W525.
:: 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.
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:: DOWNLOAD
:: MORE INFORMATION
Citation
Jarman SN (2004)
Amplicon: software for designing PCR primers on aligned DNA sequences.
Bioinformatics 20: 1644-1645.
:: DESCRIPTION
The primerD program implements a novel algorithm for the design of unique degenerate primer pairs. Using primers designed by primerD it is possible to reduce the total number of primers that need to be amplified by over 35% while amplifying the same number of targets. This program has a highly configurable set of parameters that account for both basic PCR and degenerate primer constraints. As a final verification of primer pair efficacy an extensive mis-prim.
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N/A
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:: DOWNLOAD
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:: DESCRIPTION
RNAxs is a tool especially created to design potent siRNAs.
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:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Biotechnol. 2008 May;26(5):578-83. Epub 2008 Apr 27.
The impact of target site accessibility on the design of effective siRNAs.
Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL.
