Merging the physical properties of DNA with genomic annotations in Ensembl

Abstract

On a DNA sequence, we attach information about its features and attributes, and this kind of information is called annotations. Over the past few years there has been a development to gather and group annotations to a central service, so that scientists will be able to compare all kinds of annotations. Comparisons are performed with the aim of identifying related biological features. Ensembl is such an annotation centre, and this thesis addresses the issue of integrating an annotation made by the stitch profile algorithm into Ensembl. This stitch profile algorithm is a novel way of calculating the different conformations corresponding to a DNA melting profile, i.e. modeling of the physical attributes of the DNA double helix, so that it becomes easier to see what state the DNA molecule is in. We then analyze the how accurately the stitch profiles correlate to the annotations in Ensembl.