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analyseprimer

A package to evaluate PCR and LAMP primers

https://github.com/pamella-miranda/analyseprimer

Science Score: 67.0%

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Repository

A package to evaluate PCR and LAMP primers

Basic Info
  • Host: GitHub
  • Owner: pamella-miranda
  • License: gpl-3.0
  • Language: Perl
  • Default Branch: main
  • Homepage:
  • Size: 337 KB
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Created about 1 year ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

AnalysePrimer

AnalysePrimer is a software package to evaluate DNA mismatches in primers and probes used in PCR- and LAMP-based methods and other techniques.

Given a set of primers/probes and genomes of interest, you will be able to align them and achieve all possible alignments in a perfect and mismatch way. Then, it will calculate the melting temperatures and the coverages for perfect match and up to three contiguous mismatches.

Note

A complete user manual is available here as analyseprimer-user-manual.pdf.

Installation

Download the software package

You can find the compiled binary files, for many Linux distributions, as well as source code, at this location:

https://bioinf.fisica.ufmg.br/software/

Browse to the desired version of the softwares and then download the appropriate packages for your Linux distribution. If your distribution is not covered then download the source code and compile manually, see below for instructions.

You need download and install the following software packages

  1. TfReg (version 5.3 or higher)
  2. AlignPrimer (version 1.0 or higher)
  3. analyse mismatch primers.tar.gz

The latter is a package of Bash and Perl scripts to carry AnalysePrimer out, examples of primer files and its documentation.

What will be installed?

Typically, there will be at least a binary executable file for TfReg and AlignPrimer

/usr/bin/tfreg /usr/bin/align_primer

The documentation (which you are reading right now) is located at

http://bioinf.fisica.ufmg.br/software/analysemismatchprimers.tar.gz

named analyseprimer-user-manual.pdf.

Specific instructions

All packages were fully tested for OpenSUSE 15.0 and 15.1.

  • TfReg and AlignPrimer

Download the appropriate package for your system from

https://bioinf.fisica.ufmg.br/software/

For example, if your system is 64bits, you may download the packages

http://bioinf.fisica.ufmg.br/software/tfreg-6.0/openSUSELeap42.3/TfReg-1.0-1.2.1.x8664.rpm http://bioinf.fisica.ufmg.br/software/AlignPrimer-1.0/openSUSELeap42.3/AlignPrimer-1.0-4.1.x8664.rpm

Note: version numbers may vary from this example. Then install

zypper install TfReg-1.0-1.2.1.x8664.rpm zypper install AlignPrimer-1.0-4.1.x8664.rpm

  • analysemismatchprimers

Download the source package from webpage

http://bioinf.fisica.ufmg.br/software/analysemismatchprimers.tar.gz

The package is called analysemismatchprimers.tar.gz. You need to create a new folder or put the package in the folder of your choice. Unpacking the tar package

tar -xvf analysemismatchprimers.tar.gz

The scripts and examples of primer files will be accessible.

If things go wrong

Most problems will come from missing library packages or from erroneous usage of your system. It is not possible for me to cover everything that may go wrong, so please feel free to contact me. Please include a detailed description of error messages, which system you are using and a step by step description of what you tried to do. Please understand that I will need as much information as possible. I can do nothing with messages saying simply “TfReg is not working on Ubuntu”.

Authors

Pâmella Miranda --- pamella.mm@gmail.com

Gerald Weber --- gweberbh@gmail.com

Version History

  • 0.1 --- initial release

License

This project is licensed under the MIT License. See the LICENSE.md file for details.

Citation

DOI

  • P. Miranda, G. Weber, Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes, Mol. Cell. ProbesIn press. doi:10.1016/j.mcp.2021.101707.
  • P. Miranda, V. B. Barbosa and G. Weber. Mesoscopic evaluation of DNA mismatches in PCR primer-target hybridisation to detect SARS-CoV-2 variants of concern. In Brazilian Symposium on Bioinformatics, pages 145–150. Springer, 2021. doi:10.1007/978-3-030-91814-9 15.
  • P. Miranda, P. A. Alves, R. L. do Monte-Neto and G. Weber. In silico thermodynamic evaluation of the effectiveness of RT-LAMP primers SARS-CoV-2 variants detection. The Open COVID Journal, 4(1), 2024. doi:10.2174/0126669587279780240130063422.
  • Miranda, P., & Weber, G. (2021). AnalysePrimer. Zenodo. https://doi.org/10.5281/zenodo.15345157.

Archived

SWHSWH

Owner

  • Name: Pamella Miranda
  • Login: pamella-miranda
  • Kind: user
  • Location: Belo Horizonte, Brazil

Physicist and Bioinformatician

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Miranda"
  given-names: "Pâmella"
  orcid: "https://orcid.org/0000-0001-8876-1864"
- family-names: "Weber"
  given-names: "Gerald"
  orcid: "https://orcid.org/0000-0002-2935-1571"
title: "AnalysePrimer"
version: 1.0.0
doi: 10.5281/zenodo.15345157
date-released: 2021-04
url: "https://github.com/pamella-miranda/AnalysePrimer"

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