Category: PCR / Primer Design

Assembly PCR Oligo Maker – Design Oligodeoxynucleotides For Constructing Long DNA Molecules

Assembly PCR Oligo Maker

:: 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.

::DEVELOPER

 the Johnson lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  Assembly PCR Oligo Maker

:: 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.

 

Amplicon b09 – Software for Designing PCR Primers on Aligned DNA Sequences

Amplicon b09

:: 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.

::DEVELOPER

Dr Simon Jarman

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Amplicon 

:: MORE INFORMATION

Citation

Jarman SN (2004)
Amplicon: software for designing PCR primers on aligned DNA sequences.
Bioinformatics 20: 1644-1645.

FindProbe v2 – Design Probes for Microarrays

FindProbe v2

:: DESCRIPTION

FindProbe is a software for research involves designing probes for microarrays. Existing algorithms usually select probes using the criteria of homogeneity, sensitivity, and specificity. This project proposes to include one additional criterion, uniformity, which further improves the quality of the probes selected. It makes use of some smart filtering techniques to avoid redundant computation while maintaining accuracy.

::DEVELOPER

Dr. Sung Wing Kin, Ken

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 FindProbe

:: MORE INFORMATION

Citation:

Proc IEEE Comput Soc Bioinform Conf. 2003;2:65-74.
Fast and accurate probe selection algorithm for large genomes.
Sung WK, Lee WH.

qcalculator 1.0 – Calculate Relative mRNA Gene Expression

qcalculator 1.0

:: DESCRIPTION

qCalculator is a tool to calculate relative mRNA Gene Expression.

::DEVELOPER

Ralf Gilsbach @ Institut of Pharmacology & Toxicology, University of Bonn (Ralf.Gilsbach@gmx.de)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Excel

:: DOWNLOAD

 qcalculator

:: MORE INFORMATION

 

qPCR-DAMS 1.2 – Analyze, Manage, and Store Quantitative Real-Time PCR data.

qPCR-DAMS 1.2

:: DESCRIPTION

qPCR-DAMS is a database management system implemented on MS Access 2003 and Visual Basic. It is designed to analyze, manage, and store relative and absolute quantitative real-time PCR data. The system consists of 5 blocks: three blocks (Gene, Plate, and Experiment) for inputting, storing and describing raw data, and two blocks (View data and Process Data) for checking, evaluating, and processing data. Users are allowed to choose among four basic outputs: (I) Ratio relative quantification, (II) Absolute level, (III) Normalized absolute expression, and (IV) Ratio absolute quantification, and two advanced options: (V) Multiple reference relative quantification and (VI) Multiple references absolute quantification, within single software package. The coefficient of variation is monitored at each step during data processing and the accuracy is further improved by an easy data tracking and display system. In summary, qPCR-DAMS is a handy novel tool for real-time PCR users.

::DEVELOPER

Nili Jin , Keyu He and Lin Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft Access 2000 or above

:: DOWNLOAD

 qPCR-DAMS

:: MORE INFORMATION

Citation

Nili Jin , Keyu He and Lin Liu
qPCR-DAMS: a database tool to analyze, manage, and store both relative and absolute quantitative real-time PCR data
Physiological Genomics 25:525-527 (2006)

PerlPrimer 1.1.21 – Open-source PCR Primer Design

PerlPrimer 1.1.21

:: DESCRIPTION

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.

::DEVELOPER

Owen Marshall at Murdoch Childrens Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PerlPrimer

:: MORE INFORMATION

Citation

Owen J. Marshall
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Bioinformatics (2004) 20 (15): 2471-2472.

DART-PCR 1.0 – Quantitative Real-time PCR Data Analysis

DART-PCR 1.0

:: DESCRIPTION

DART-PCR (Data Analysis for Real‐Time PCR) provides a simple means of analysing real-time PCR data from raw flurescence data. This allows an automatic calculation of amplification kinetics, as well as performing the subsequent calculations for relative quantification and calculation of assay variability. Amplification efficiencies are also tested to dtect anomalus samples within groups (outlayers) and differences between experimatal groups (amplification equivalence).

::DEVELOPER

Stuart N. Peirson, Jason N. Butler and Russell G. Foster

:: SCREENSHOTS

:: REQUIREMENTS

  • Excel

:: DOWNLOAD

 DART-PCR

:: MORE INFORMATION

Citation

Stuart N. Peirson, Jason N. Butler and Russell G. Foster (2003)
Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
Nucl. Acids Res. (2003) 31 (14): e73

primerD 1.0 – Design of Unique Degenerate Primer Pairs

primerD 1.0

:: 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.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 primerD

:: MORE INFORMATION

MaxAlike 1.0 – Phylogenetic Reconstruction of incomplete Sequences by Maximum Likelihood

MaxAlike 1.0

:: DESCRIPTION

MaxAlike algorithm aims at reconstructing a nucleotide sequence in a target species, based on a multiple sequence alignment and a phylogenetic tree of homologous sequences from other species. For each alignment position the probabilities of occurrence for each nucleotide are computed, considering the phylogenetic position of the target species in the tree.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxAlike

:: MORE INFORMATION

Citation:

P. Menzel, P. F. Stadler and J. Gorodkin:
maxAlike: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences,
Bioinformatics, 2011, 27, 317-325.