Seminar Genome; Sequencing, Assembly & Annotation
Introduction
The seminar Genome; Sequencing, Assembly & Annotation will provide deeper insight in what a genome sequence comprises, and explain its dynamic nature. To obtain a genome sequence in general, the orders of base pairs are deduced from fragments of DNA following chemical or physical reactions (sequencing). The orders of the fragments are in turn linked using programs that calculate the most likely linkages based on statistics (assembly). Finally, patterns are searched in and recorded for the assembled fragments (annotation). Together this will result in an approximation of the physical genetic map of the sequenced individual and the encoded information herein.
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Obtaining a fully complete and error-free genome sequence is virtually impossible, and even a good approximation is often a complicated and costly endeavour. It is therefore wise to select an approach that optimizes those aspects of the genome sequence that are most important for the success of a given project. One should realize that obtaining a genome sequence by itself is seldom the goal, but instead is a mean to achieve a goal. In this seminar we will investigate the currently leading sequencing, assembly and annotation methods, examine their benefits and drawbacks, and explore possibilities for their combination.
The seminar contains three componentsContent:
(1) Basics, performed individually. Reading of the review A field guide to whole-genome sequencing, assembly and annotation, Ekblom et al., 2014.https://doi.org/10.1111/eva.12178 and answering of the accompanying general questions about genome sequencing, assembly and gene prediction. Some of the questions require a little extra information outside of the indicated review, which can be obtained by searching the internet (e.g. through Google).
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