Array Designer 4.43 – Oligo & cDNA Microarray Design Software

Array Designer 4.43

:: DESCRIPTION

Array Designer designs thousands of primers and probes for oligo and cDNA microarrays in seconds. It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

Array Designer Demo

:: MORE INFORMATION

Oligo 7.60 – Primer Analysis Software

Oligo 7.60

:: DESCRIPTION

OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo’s search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers.  Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis. OLIGO performs a range of functions for researchers in PCR and related technologies; consensus, multiplex and degenerate primers, oligonucleotide database, secondary structure, LCR and more.

::DEVELOPER

Molecular Biology Insights

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

Oligo

:: MORE INFORMATION

MODEST 0.1.4-10 – MAGE Oligo Design Tool

MODEST 0.1.4-10

:: DESCRIPTION

MODEST allows the rapid and effective design of optimal MAGE (multiplex automated genome engineering) oligos based on simple input, to achieve any mutation possible with MAGE.

::DEVELOPER

the Sommer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.
Bonde MT, Klausen MS, Anderson MV, Wallin AI, Wang HH, Sommer MO.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W408-15. doi: 10.1093/nar/gku428

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

PROBER

:: 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

DEODAS 0.2.0 -DEgenerate Oligo Nucleotide Design & Analysis System

DEODAS 0.2.0

:: 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

Karl Diedrich

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • gtkmm, available at http://gtkmm.sourceforge.net/
  • libsigc++, available at http://libsigc.sourceforge.net/
  • python
  • pygtk
  • pygnome
  • postgresql

:: DOWNLOAD

 DEODAS

:: MORE INFORMATION

Citation

Karl Diedrich
DEODAS: A DEgenerate Oligonucleotide Design and Analysis System 

BIOSAP 0.1.7 – Generate Oligos for the Inkjet Arrayer

BIOSAP 0.1.7

:: DESCRIPTION

BIOSAP (Blast Integrated Oligonucleotide Selection Accelerator Package) generate oligos for the Inkjet Arrayer. BIOSAP provides the opportunity to design thousands of oligonucleotides to a given set of biological DNA sequences. The features (oligos) reported are guaranteed to be unique among all features chosen, have certain properties based on the requirements specified by the user, are checked for potential self-hybridizing properties, and are BLAST (Altschul et al., 1990) searched for possible close alignments to genomic sequences other than one for which the given feature was chosen. The final output of BIOSAP is an XML document containing the details and results of the search. This data can be imported into a database to be searched for future iterations of microarray design.

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BIOSAP

:: MORE INFORMATION

N/A

LOCK 1.2 – Locater of Oligos

LOCK 1.2

:: DESCRIPTION

LOCK Locates user-specified oligonucleotide patterns within a larger sequence. For example, restriction digest sites and fragment sizes can be determined for a plasmid or genome.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac Os / Linux
  • Perl
  • TK

:: DOWNLOAD

LOCK ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

FOCK 1.0 – Frequency of Oligos

FOCK 1.0

:: DESCRIPTION

FOCK Analyzes a FASTA sequence for n-mer frequency (specified by user). Useful for identifying common or rare restriction sites, etc.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

Command-line interface.

:: REQUIREMENTS

:: DOWNLOAD

FOCK for Win ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.