Short tandem repeats (STRs) are hypervariable elements in the genome that often vary in repeat length between individuals. STRs consist of simple repeated sequenced such as for example AC (di-nucleotide) or ACC (tri-nucleotide) and are present throughout the genomes of most species. Many STRs are found close to, or even within, the coding regions of genes (tri-nucleotide repeats), and it has been shown that some STRs (length variants) can affect gene regulation or protein function. Thus, STR length variation may be associated with or even be causal mutations for adaptation to specific environments (and changing environments). In our group we have investigated STR length variations and their effects in natural populations of Arabidopsis thaliana and Atlantic cod (Gadus morhua) using whole genome sequencing data. However, scoring length variants of STRs possess challenges due to the sequencing method (short reads). We are therefore in the process of changing from short read to the use of long read (single molecule) sequencing in STR analyses.
We are seeking one master student: The master student will be involved in investigating the accuracy and the use of bioinformatic and statistic tools to evaluate the use of long read sequencing in STR analyses. Will long reads facilitate detection of many more STRs undetectable or non-scorable with short reads? This is a central question. Both Arabidopsis and Atlantic cod will be investigated. An interest in (or interest of learning) bioinformatics, modelling and statistical methods will be a good starting point. The master project will be part of a larger project investigating STRs across the tree of life and functional implications – and there will be a team of researchers (PhDs, post docs, researchers) at CEES as well as internationally.
What you will learn: You will learn bioinformatics, statistical methods and evolutionary genomics – and get experience in scientific team-work. With a training in bioinformatics and statistics you will be very attractive for jobs in academia and outside.
What we offer: We offer a friendly and kind mentoring environment with a lot of experience in supervising master students. We also offer the possibility of joining research schools such as the NORBIS and Digital Life Research School and to attend international courses fitting your master project.
Supervisors: Kjetill S Jakobsen and Wiliam B Reinar