Reference Work Entry

Encyclopedia of Algorithms

pp 1383-1386

Date:

Multiplex PCR for Gap Closing (Whole-Genome Assembly)

  • Vera AsodiAffiliated withCenter for the Mathematics of Information, California Institute of Technology

Keywords

Multiplex PCR Whole genome assemble

Years and Authors of Summarized Original Work

  • 2002; Alon, Beigel, Kasif, Rudich, Sudakov

Problem Definition

This problem is motivated by an important and timely application in computational biology that arises in whole-genome shotgun sequencing. Shotgun sequencing is a high throughput technique that has resulted in the sequencing of a large number of bacterial genomes as well as Drosophila (fruit fly) and Mouse and the celebrated Human genome (at Celera) (see, e.g., [8]). In all such projects, one is left with a collection of DNA fragments. These fragments are subsequently assembled, in-silico, by a computational algorithm. The typical assembly algorithm repeatedly merges overlapping fragments into longer fragments called contigs. For various biological and computational reasons some regions of the DNA cannot covered by the contigs. Thus, the contigs must be ordered and oriented and the gaps between them must be sequenced using slower, more tedious methods. For further details see, e.g.,  ...

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