This repository contains Jupyter notebooks describing cloning using Python, Jupyter notebooks, Biopython and pydna.
The notebooks and other files in this repository accompany the publication:
Silva, P.C., Ceja-Navarro, J.A., Azevedo, F. et al. A novel D-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae. Sci Rep 11, 4766 (2021). https://doi.org/10.1038/s41598-021-83937-z
The notebooks can be visualized in a number of ways. Each notebook (.ipynb) is accompanied by a HTML file with the same name but with an (.html) extension. These can be opened in a web browser without installing any software.
The notebooks (.ipynb) can be opened in the browser through the nbviewer service here or directly in Github here.
pYPK7_TEF1_RPS7B Yeast expression vector with TEF1 promoter and KanMX4 marker. This vector was used as a source for the promoter and terminator for the pLBL2 and pLBL3 plasmids.
pLBL2 Yeast expression vector with TEF1 promoter, RPS7B terminator and a URA3 marker.
pLBL3 Same as pLBL2 but with the URA3 marker replaced by a LEU2 marker.
Each notebook contain links (usually in the end) to the resulting sequences in Genbank flat file format.
These notebooks are tested on the github action build service.
This means that the notebook outputs are re-executed and compared with saved results once per week to ensure reproducibility.
If the badge below is green, all tests gave the expected results.
For each Jupyter notebook file, there is a html version with the same name but with a
.html extension instead of .ipynb. These files are static and can be viewed with any
modern web browser.
We are grateful for funding from:
Fundação para a Ciência e Tecnologia Portugal (FCT) through project FatVal PTDC/EAM-AMB/032506/2017 funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 – Programa Operacional Competitividade e Internacionalizacão (POCI).
CBMA was supported by the strategic program UIDB/04050/2020 funded by national funds through the FCT I.P.