Sequence Analysis in the Biomedical Domain

The MetaGraph Project

Despite the massive data availability due to fast and affordable high-throughput DNA and RNA sequencing, a central problem remains that can be stated as a simple question: Given a short DNA sequence arising from experimental measurement, have we ever seen this sequence before? Followed closely by a second question: What information about this sequence can be derived or inferred from the knowledge currently available in the domain? The MetaGraph project not only aims to answer these questions but also to do so promptly while using minimal computing and storage resources. [Read more...]

Sequence Comparison

Assessing the exact or approximate distance between two given biological sequences (DNA, RNA, amino acid, etc.) or parts thereof is a ubiquitous task in sequence bioinformatics. Depending on the application domain, exact local or global alignments are required, or an approximate estimation of their distance suffices. We are interested in both ends of this spectrum. [Read more...]

Selective Sequencing

Along with the recent developments in long-read and single-molecule sequencing, new technological features have appeared. For example, Oxford Nanopore Technologies (ONT), allows one to drop the sequencing of a single molecule at any time point after the reading has begun and so enables selective sequencing. This interactive way of measuring a sequence opens up many new use cases and poses interesting bioinformatics problems. [Read more...]