Shotgun sequencing (hierarchial shotgun sequencing)

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Although shotgun sequencing can in theory be applied to a genome of any size, its direct application to the sequencing of large genomes (for instance, the Human Genome) was limited until the late 1990s, when technological advances made practical the handling of the vast quantities of complex data involved in the process.[9] Historically, full-genome shotgun sequencing was believed to be limited by both the sheer size of large genomes and by the complexity added by the high percentage of repetitive DNA (greater than 50% for the human genome) present in large genomes.[10] It was not widely accepted that a full-genome shotgun sequence of a large genome would provide reliable data. For these reasons, other strategies that lowered the computational load of sequence assembly had to be utilized before shotgun sequencing was performed.[10] In hierarchical sequencing, also known as top-down sequencing, a low-resolution physical map of the genome is made prior to actual sequencing. From this map, a minimal number of fragments that cover the entire chromosome are selected for sequencing.[11] In this way, the minimum amount of high-throughput sequencing and assembly is required.

The amplified genome is first sheared into larger pieces (50-200kb) and cloned into a bacterial host using BACs or PACs. Because multiple genome copies have been sheared at random, the fragments contained in these clones have different ends, and with enough coverage (see section above) finding a scaffold of BAC contigs that covers the entire genome is theoretically possible. This scaffold is called a tiling path. Source of the article published in description is Wikipedia. I am sharing their material. Copyright by original content developers.
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