Bilkent University
Department of Computer Engineering

---

CS 590/690 SEMINAR

 

Structural Variation Detection by Assembly-to-Assembly Comparison

 

Rafi Çoktalaş

Master Student
(Supervisor: Assoc.Prof.Can Alkan)
Computer Engineering Department
Bilkent University

Abstract: Structural variants (SVs) are genomic alterations in DNA of length ranging from hundreds to millions of nucleotides, and are a major source of genetic variation. SVs can arise from diverse mechanisms and can cause developmental disorders, cancer, and evolutionary divergence. Due to their large size, complex nature and effects on gene expression, accurate detection of SVs in genome assemblies is a challenging but an important task. Our proposed approach for SV discovery is based on the mapping of k-mers in a query genome assembly to a reference genome assembly using minimizers, which are short subsequences that are similar if produced by similar sequences. This mapping constitutes a geometrical model and by incorporating a plane-sweep algorithm, the algorithm can further refine and classify the SVs based on their size, orientation, and other properties.

 

DATE: April 24, Monday @ 15:30 Place: Zoom