PrimeDesign 0.2 – Flexible Design of pegRNAs and ngRNAs for Prime Editing

PrimeDesign 0.2

:: DESCRIPTION

PrimeDesign is a software tool for the flexible and comprehensive design of prime editing. PrimeDesign is an edit-centric design tool for the installation of substitution, insertion, and deletion edits, and is generalizable for both single and combinatorial edits. Taking a single input that encodes both the reference and edit sequence, PrimeDesign enumerates all possible pegRNA protospacers, pegRNA extensions, and ngRNAs within set parameter ranges to install the desired edit(s).

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • Docker

:: DOWNLOAD

PrimeDesign

:: MORE INFORMATION

Citation

Hsu JY, Grünewald J, Szalay R, Shih J, Anzalone AV, Lam KC, Shen MW, Petri K, Liu DR, Joung JK, Pinello L.
PrimeDesign software for rapid and simplified design of prime editing guide RNAs.
Nat Commun. 2021 Feb 15;12(1):1034. doi: 10.1038/s41467-021-21337-7. PMID: 33589617; PMCID: PMC7884779.

Auto-qPCR – Process Spreadsheet output directly from qPCR Thermocycler

Auto-qPCR

:: DESCRIPTION

Auto-qPCR is a python based web app designed to process raw data files from thermal cycler machines.

::DEVELOPER

Auto-qPCR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Auto-qPCR

:: MORE INFORMATION

Citation

Maussion G, Thomas RA, Demirova I, Gu G, Cai E, Chen CX, Abdian N, Strauss TJP, Kelaï S, Nauleau-Javaudin A, Beitel LK, Ramoz N, Gorwood P, Durcan TM.
Auto-qPCR; a python-based web app for automated and reproducible analysis of qPCR data.
Sci Rep. 2021 Oct 29;11(1):21293. doi: 10.1038/s41598-021-99727-6. PMID: 34716395; PMCID: PMC8556264.

Ex-Ex Primer – Designing Oligonucleotides Spanning Spliced Nucleic Acid Regions

Ex-Ex Primer

:: DESCRIPTION

Ex-Ex Primer is a new computational program which offers many improved, user-friendly features, and reliably creates junction primers and probes.

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Govindkumar B, Kavyashree B, Patel K, Sasidharan K, T SA, Thomas L, Bkg P, Hn R, R M, Acharya KK.
Ex-Ex Primer: an experimentally validated tool for designing oligonucleotides spanning spliced nucleic acid regions from multiple species.
J Biotechnol. 2021 Oct 28:S0168-1656(21)00277-7. doi: 10.1016/j.jbiotec.2021.10.009. Epub ahead of print. PMID: 34756973.

nondetects 2.22.0 – Model and Impute non-detects in qPCR data

nondetects 2.22.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239

UniPrime2 2.10 – Universal Primer Design Server

UniPrime2 2.10

:: DESCRIPTION

UniPrime2 is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR. UniPrime2 automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime2 differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program.

::DEVELOPER

UniPrime2 team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 UniPrime2

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W209-13. Epub 2009 Apr 28.
UniPrime2: a web service providing easier Universal Primer design.
Boutros R, Stokes N, Bekaert M, Teeling EC.

AutoDimer 1.0 – Screening Tool for Primer-dimer & Hairpin Structures

AutoDimer 1.0

:: DESCRIPTION

AutoDimer software was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (< 30 nucleotides). AutoDimer was originally created to assist in the development of multiplex PCR assays for probing STR and SNP markers for forensic purposes.

::DEVELOPER

Peter M. Vallone

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AutoDimer

:: MORE INFORMATION

Citation

Vallone, P.M. and Butler, J.M. (2004)
AutoDimer: a screening tool for primer-dimer and hairpin structures.
Biotechniques, 37(2): 226-231.

DefiningTheRain – Automatically analysing BioRad’s Digital Droplet PCR Output

DefiningTheRain

:: DESCRIPTION

Defining The Rain is a javascript program that allows user to cluster digital droplet PCR data to define cut offs and improve calling

::DEVELOPER

DefiningTheRain team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • javascript

:: DOWNLOAD

  DefiningTheRain

:: MORE INFORMATION

Citation

Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, ‘definetherain’.
Jones M, Williams J, G?rtner K, Phillips R, Hurst J, Frater J.
J Virol Methods. 2014 Jun;202:46-53. doi: 10.1016/j.jviromet.2014.02.020.

GenoFrag 2.1 – Design Primers Optimized for Whole Genome Scanning by Long-range PCR Amplification

GenoFrag 2.1

:: DESCRIPTION

GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in ~10 kb‐long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.

::DEVELOPER

GenoFrag Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Unix/MacOsX
  • Python

:: DOWNLOAD

 GenoFrag Source Code

:: MORE INFORMATION

Citation

Nouri Ben Zakour et. al.
GenoFrag: software to design primers optimized for whole genome scanning by long‐range PCR amplification
Nucl. Acids Res. (2004) 32 (1): 17-24

LAMP Designer 1.16 – Design Primers for Loop-Mediated Isothermal Amplification Assays

LAMP Designer 1.16

:: DESCRIPTION

LAMP Designer designs efficient primers for Loop-Mediated Isothermal Amplification assays, that amplify DNA and RNA sequences at isothermal conditions, eliminating the necessity of a PCR setup. The technology relies on auto-cycling and DNA polymerase mediated strand displacement DNA synthesis, amplifying a few copies of DNA to 109 in less than an hour. Reverse transcription coupled LAMP can be applied for amplification of RNA sequences.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

LAMP Designer Demo

:: MORE INFORMATION

GenEx 7.0 – Analyze Real-time qPCR Data

GenEx 7.0

:: DESCRIPTION

GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis.

::DEVELOPER

MultiD Analyses AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GenEx

:: MORE INFORMATION

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