Training in bioinformatics and data analysis 11-15 April 2016
Damien MEYER, researcher in microbiology from CIRAD team in Guadeloupe, assisted to training in bioinformatics and data analysis, organized by CIRAD and INRA and funded by Epigenesis project. This training was held in Nantes (UMR BIOEPAR), France from 11th to 15th of April.
During 5 days of training, Damien used Python coding to work on two topics:
- Download a Genbank format sequence file (Ehrlichia ruminantium genome as an example) and construction of an object oriented script to extract intergenic regions and promoters;
- Genomic datasets manipulation and introduction to comparative genomics – construction of a Python script to extract protein sequences of 4 genomes and to compare them to generate a Venn Diagramm (using Matplotlib) indicating conserved and specific proteins.
The main goals of this training was: to let participants to be able to construct autonomously basic scripts to analyze genomic sequences; to create publication-ready figures; to launch a blast on a Linux environment and with a Python script but also to be familiar with object oriented programming and be able to use the Python online resources.
In a near future it will be proposed: auto-formation of the participant, thanks to the numerous online resources and advanced courses for confirmed participants and train them of software versioning (GIT) and automated tests.
