PrimerSeq 1.1.12 – Primer Seek in RNA-Seq

PrimerSeq 1.1.12

:: DESCRIPTION

PrimerSeq designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data.

::DEVELOPER

Xing Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 PrimerSeq

:: MORE INFORMATION

Citation

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
Tokheim C, Park JW, Xing Y.
Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001.

Disperse 1.0.3 – Design of Selector Assays for Targeted Resequencing Applications

Disperse 1.0.3

:: DESCRIPTION

The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes

::DEVELOPER

Disperse Team

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows / Linux
  • Java
  • Perl
  • Blast

:: DOWNLOAD

 Disperse

:: MORE INFORMATION

Citation

J. Stenberg, M. Zhang and H. Ji
Disperse–a software system for design of selector probes for exon resequencing applications
Bioinformatics (2009) 25(5): 666-667

unifiedWMWqPCR 1.28.0 – Unified Wilcoxon-Mann Whitney Test for testing differential Expression in qPCR data

unifiedWMWqPCR 1.28.0

:: DESCRIPTION

unifiedWMWqPCR implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

::DEVELOPER

Jan R. De Neve & Joris Meys <Joris.Meys at UGent.be>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 unifiedWMWqPCR

:: MORE INFORMATION

Citation

unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R.
De Neve J, Meys J, Ottoy JP, Clement L, Thas O.
Bioinformatics. 2014 May 2. pii: btu313.

Primegens 2.0.5 – Primer Design for Microarray

Primegens 2.0.5

:: DESCRIPTION

Primegens ((PRIMEr Design Using GEN Specific Fragments) is a software for high-throughput primer and probe design. The program uses two third party executables like Primer3 and Megablast.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Primegens

:: MORE INFORMATION

Citation

Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi and Dong Xu.
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation pattern of CpG island“.
Bioinformatics 2008 24(17):1837-42.

Beacon Designer 8.21 – Automate Real Time PCR Primer & Probe Design

Beacon Designer 8.21

:: DESCRIPTION

Beacon Designer automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

Beacon Designer Demo

:: MORE INFORMATION

ReadqPCR / NormqPCR 1.38.0 / – Read qPCR data / Functions for Normalisation of RT-qPCR data

ReadqPCR / NormqPCR 1.38.0

:: DESCRIPTION

ReadqPCR and NormqPCR are R/Bioconductor packages to analyse RT-qPCR data.

::DEVELOPER

James Perkins <j.perkins at ucl.ac.uk>, Matthias Kohl, Nor Izayu Abdul Rahman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 ReadqPCR and NormqPCR

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Jul 2;13:296. doi: 10.1186/1471-2164-13-296.
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
Perkins JR1, Dawes JM, McMahon SB, Bennett DL, Orengo C, Kohl M.

CloningBench 3.2.0 – Guide of Cloning Experiments for iPhone / iPAD

CloningBench 3.2.0

:: DESCRIPTION

The CloningBench mobile app is designed to provide you with useful and essential tools to help guide your cloning experiments.

:DEVELOPER

Thermo Fisher Scientific Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • iPhone /  iPod touch / iPad

:: DOWNLOAD

 CloningBench

:: 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

PrimerPlex 2.76 – Oligo Design for Multiplex PCR

PrimerPlex 2.76

:: DESCRIPTION

PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex assays. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both the time and cost of experimentation.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

PrimerPlex Demo

:: MORE INFORMATION

3PD – Primer design for Chromosome Conformation Capture Assays

3PD

:: DESCRIPTION

3PD is a bioinformatics solution  to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 29;10:635. doi: 10.1186/1471-2164-10-635.
3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Fröhler S, Dieterich C.