Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/ipb-halle/goldenmutagenesis

Support for rapid design of primers for amino acid exchanges and saturation mutagenesis by Golden Gate cloning.
https://github.com/ipb-halle/goldenmutagenesis

goldengate primer primer-design

Last synced: 23 days ago
JSON representation

Support for rapid design of primers for amino acid exchanges and saturation mutagenesis by Golden Gate cloning.

Host: GitHub
URL: https://github.com/ipb-halle/goldenmutagenesis
Owner: ipb-halle
License: lgpl-3.0
Created: 2018-09-04T15:23:15.000Z (over 6 years ago)
Default Branch: master
Last Pushed: 2021-04-08T11:49:23.000Z (over 3 years ago)
Last Synced: 2024-07-30T19:59:39.948Z (5 months ago)
Topics: goldengate, primer, primer-design
Language: R
Homepage: https://ipb-halle.github.io/GoldenMutagenesis/
Size: 6.33 MB
Stars: 4
Watchers: 5
Forks: 3
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        README

================

Chris Ulpinnis & Pascal Püllmann

2020-03-05

[![Travis-CI Build Status](https://travis-ci.org/ipb-halle/GoldenMutagenesis.svg?branch=master)](https://travis-ci.org/ipb-halle/GoldenMutagenesis)

[![GitHub license](https://img.shields.io/github/license/ipb-halle/GoldenMutagenesis)](https://github.com/ipb-halle/GoldenMutagenesis/blob/master/LICENSE)

[![GitHub release (latest by date)](https://img.shields.io/github/v/release/ipb-halle/GoldenMutagenesis)](https://github.com/ipb-halle/GoldenMutagenesis/releases)

[![GitHub issues](https://img.shields.io/github/issues/ipb-halle/GoldenMutagenesis)](https://github.com/ipb-halle/GoldenMutagenesis/issues)

# GoldenMutagenesis



## Abstract

The Golden Gate cloning technique has been proven to be a highly

efficient toolbox for a variety of cloning setups. Based on its modular

concept it is particularly suitable for the use in multiple-site

mutagenesis approaches. In this technical note we developed a protocol

termed Golden Mutagenesis for the rapid, easy, reliable and cheap

formation of mutagenesis libraries. One to five positions could be

altered in parallel or simultaneously within two days. To facilitate the

implementation of this technique, this R-library has been developed for

the automated primer design and the graphical evaluation of sequencing

results to determine the quality of the library.  

The publication is available at https://rdcu.be/bMfta. 

## Web-interface

A web-based user-interface is available at https://msbi.ipb-halle.de/GoldenMutagenesisWeb.

The GitHub page of the webinterface can be found at https://github.com/ipb-halle/GoldenMutagenesisWeb.

A docker container containing the web interface can be found at https://hub.docker.com/r/sneumann/goldenmutagenesisweb.

## Installation

You can install GoldenMutagenesis from GitHub with:

``` r

# install.packages("devtools")

devtools::install_github("ipb-halle/GoldenMutagenesis")

```

## Documentation

The documentation can be accessed at https://ipb-halle.github.io/GoldenMutagenesis/.

## Examples

### Vignettes

To start with this library we recommend to take a look at our

vignettes\!  

[Point

Mutagenesis](https://ipb-halle.github.io/GoldenMutagenesis/articles/Point_Mutagenesis.html)  

[Multiple Site Directed Mutagenesis -

Example1](https://ipb-halle.github.io/GoldenMutagenesis/articles/MSD.html)  

[Multiple Site Directed Mutagenesis -

Example2](https://ipb-halle.github.io/GoldenMutagenesis/articles/MSD2.html)  

[Multiple Site Directed Mutagenesis -

Example3](https://ipb-halle.github.io/GoldenMutagenesis/articles/MSD3.html)  

[Quick Quality

Control](https://ipb-halle.github.io/GoldenMutagenesis/articles/QQC.html)  

### Jupiter Notebooks at binder

You can also use predefined Jupiter notebooks on binder to use the library.

#### Multiple Site Directed Mutagenesis

[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/ipb-halle/GoldenMutagenesis/binder?filepath=notebooks%2FMSD_USER.ipynb)

#### Single Point Mutagenesis

[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/ipb-halle/GoldenMutagenesis/binder?filepath=notebooks%2FSPM_USER.ipynb)

#### Domestication only

[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/ipb-halle/GoldenMutagenesis/binder?filepath=notebooks%2FDomesticate_only_USER.ipynb)