Category: PCR / Primer Design

LinRegPCR 20210614 – Analysis of Quantitative PCR Data

LinRegPCR 20210614

:: DESCRIPTION

LinRegPCR is a program for the analysis of quantitative RT-PCR (qPCR) data resulting from monitoring the PCR reaction with SYBR green or similar fluorescent dyes. The program determines a baseline fluorescence and does a baseline subtraction. Then a Window-of-Linearity is set and PCR efficiencies per sample are calculated. With the mean PCR efficiency per amplicon, the Ct value per sample and the fluorescence threshold set to determnine the Ct, the starting concentration per sample, expressed in arbitrary fluorescence units, is calculated

::DEVELOPER

J. M. Ruijter, S. van der Velden,A. Ilgun @ Heart Failure Research Center (HFRC)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Excel

:: DOWNLOAD

 LinRegPCR

:: MORE INFORMATION

Citation

Ramakers C, Ruijter JM, Deprez RH, Moorman AF. (2003)
Assumption-free analysis of quantitative real-time PCR data
Neurosci Lett 2003 Mar 13;339(1): 62-66

AlleleID 7.85 – Assay Design for Bacterial Identification

AlleleID 7.85

:: DESCRIPTION

AlleleID® is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

AlleleID Demo

:: MORE INFORMATION

AmplifX 2.1.1 – Manage & Design Primers for PCR

AmplifX 2.1.1

:: DESCRIPTION

AmplifX is a software to search through a collection of primers, such as any molecular biologist has in his refrigerators, to find those which can be use to amplify a fragment into a target sequence, for example, and particularly, to design strategies to screen recombinant clones by PCR. Some information is associated with each primer; some automaticelly computed by AmplifX (like TM, Quality, length) and others given by the user (name, comments,…) This allows general aspects of primer management (sequences and real tubes). AmplifX can also design new primers.

::DEVELOPER

Nicolas Jullien

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX / Linux

:: DOWNLOAD

 AmplifX

:: MORE INFORMATION

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5 – Primer Design and Sequence Analysis for High-throughput Scanning Mutagenesis

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5

:: DESCRIPTION

AAscan, PCRdesign and MutantChecker is a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.

AAScan (formely AlaScan) – batch primer design software for scanning mutagenesis
MutantChecker – helps to analyse the sequenceing results from scanning mutagenesis
PCR Cloning – design of primers for ligation-independent cloning

::DEVELOPER

Laboratory of Biomolecular Research (LBR)

:: SCREENSHOTS

aascan

MutantChecker

PCRCloning

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AAScan, MutantChecker , PCR Cloning

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 30;8(10):e78878. doi: 10.1371/journal.pone.0078878. eCollection 2013.
AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
Sun D1, Ostermaier MK, Heydenreich FM, Mayer D, Jaussi R, Standfuss J, Veprintsev DB.

Oligospawn – Oligo Design from large-scale cDNA Sequences

Oligospawn

:: DESCRIPTION

OligoSpawn is an efficient software for selecting two types of oligos, namely unique and popular oligos, from large unigene databases.

::DEVELOPER

Jie Zheng, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2006 Jan 9;7:7.
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
Zheng J1, Svensson JT, Madishetty K, Close TJ, Jiang T, Lonardi S.

PrimerDesign-M – Multiple-alignment based Multiple-primer Design tool

PrimerDesign-M

:: DESCRIPTION

PrimerDesign-M was developed to meet the demands of primer design for highly variable sets of aligned sequences. It includes design requirements for next-generation sequences (NGS) including 454 sequences. It can also be used for primer and probe design for PCR, Sanger sequencing, and other systems with custom barcodes and DNA handles for universal primer annealing. The tool will design several alternative primer sets, whenever possible.

::DEVELOPER

PrimerDesign-M team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.
Yoon H, Leitner T.
Bioinformatics. 2014 Dec 17. pii: btu832.

GenomeMasker 1.3 / GenomeTester 1.3 / SNPmasker 1.1 – Design Unique Genomic PCR Primers

GenomeMasker 1.3 / GenomeTester 1.3 / SNPmasker 1.1

:: DESCRIPTION

The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.

GenomeTester (gtester) is the program that tests 1) whether PCR primers have excessive number of binding sites on template sequence and 2) how many PCR products would be amplified from the template DNA and where are they located.

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GENOMEMASKER

:: MORE INFORMATION

Citation:

Methods Mol Biol. 2015;1275:1-16. doi: 10.1007/978-1-4939-2365-6_1.
Fast masking of repeated primer binding sites in eukaryotic genomes.
Andreson R1, Kaplinski L, Remm M.

Andreson R., Reppo E., Kaplinski L., Remm M.
GENOMEMASKER package for designing unique genomic PCR primers.
BMC Bioinformatics 2006, 7:172.

PCRduplicates – Estimate PCR Duplication Rate from High-throughput Sequencing data

PCRduplicates

:: DESCRIPTION

PCRduplicates is a computational method to estimate the PCR duplication rate in high-throughput DNA sequencing experiments

::DEVELOPER

Bansal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PCRduplicates

:: MORE INFORMATION

Citation

Bansal V.
A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.
BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):43. doi: 10.1186/s12859-017-1471-9. PMID: 28361665; PMCID: PMC5374682.

PRISE – Designing Sequence-selective PCR Primers

PRISE

:: DESCRIPTION

PRISE (PRImer Selector) is an interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3′ end of the primers – a property that is crucial for sequence selectivity / specificity

::DEVELOPER

Rachid Ounit, Algorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

PRISE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PRISE

:: MORE INFORMATION

Citation

J Microbiol Methods. 2008 Mar;72(3):263-7. doi: 10.1016/j.mimet.2007.12.004.
PRISE (PRImer SElector): software for designing sequence-selective PCR primers.
Fu Q1, Ruegger P, Bent E, Chrobak M, Borneman J.