Intern Protein Modeling

Open pdf here

KeyGene – the crop innovation company
KeyGene is the go-to AgBiotech company for higher crop yield & quality. With our intellectual capital, solution driven approach and collaborative spirit, we work for the future of global agriculture with partners in the AgriFood sector. We support customers and partners with the development of new, improved crops by providing cutting edge breeding technologies, bioinformatics expertise and plant-based trait platforms. KeyGene employs more than 135 people and has sites in Wageningen, the Netherlands and in Rockville, USA. To support the research in Bioinformatics & Modeling in Wageningen we are looking for a MSc student Bioinformatics/Molecular Biology to strengthen our team:

Intern Protein Modeling

Vacancy number 16.intern002

Introduction
Since the cost for genome sequencing is dropping while the quality is rising, more and more opportunities arise for breeding companies to perform a variance identification analysis of their germplasm against a reference sequence. This analysis can easily lead to the detection of millions of variations, for a large part consisting of Single Nucleotide Polymorphisms (SNPs). The biologically more interesting SNPs are the ones in coding or regulatory regions of the genome with a putative effect on a change in gene function. In order to interpret and rank the SNPs several approaches are available to predict their impact, specifically for a damaging effect. What is currently missing is the ability to predict if mutations have a beneficial effect on the function of a protein.

Tasks
The goal of this trainee period is to make an inventory of available SNP gain of function prediction methods and to select, test and demonstrate additional methods to be used. Furthermore, a decision mechanism should be developed to predict the overall impact of an SNP, given all prediction approaches used. Where possible, variations such as insertion/deletions and presence-absence variation will be taken into account. In addition, protein structure (3D) prediction approaches will be explored which can inform predictions concerning a more precise mode of action.

Your qualifications
1. MSc student Bioinformatics, Molecular Biology or similar
2. Knowledge of Python or Perl
3. Basic knowledge of Linux shell scripting
4. Knowledge of protein modeling
5. Good communication skills in English

Duration and location
The internship will have a duration of 6 months and location will be Wageningen.

More information
If you are interested in this position you can send your letter of application and resume to:
KeyGene, Attn. Ms Tiny Swemers, Personnel Advisor, P.O. Box 216, 6700 AE Wageningen, The Netherlands or by email ts@keygene.com. Please mention the vacancy number 16.intern002 in your application.