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Physical Mapping of Chromosomes Using Unique Probes Farid Alizadeh \Lambda Richard M. Karp \Lambdayz Deborah K. Weisser y Geoffrey Zweig yz
 

Summary: Physical Mapping of Chromosomes Using Unique Probes
(Draft)
Farid Alizadeh \Lambda Richard M. Karp \Lambdayz Deborah K. Weisser y Geoffrey Zweig yz
December 9, 1994
1 Introduction
1.1 The Physical Mapping Problem
In this paper we present several combinatorial algorithms for reconstructing a DNA strand given a
collection of overlapping fragments of the strand. A human chromosome, which is a DNA molecule of
about 10 8 base pairs, is too long to be studied in its entirety and must be broken into fragments or clones.
Depending on the cloning technology used, the sizes of the clones may be as small as 3; 000 base pairs or
as large as 2; 000; 000 base pairs. Information is gathered from the individual clones, and then the DNA is
reconstructed by mathematically determining the positions of the clones.
The goal of physical mapping is to infer how the clones overlap to form the DNA molecule, given data
about each clone. The present paper focuses on the Sequence Tagged Site (STS) mapping strategy, which is
widely used for physical mapping within the Human Genome Project and other related molecular biology
projects [PSM + 91], [MCG + 93]. In particular the recent mapping of human chromosome 21 [CRG + 92]
and human chromosome Y [VFH + 92, FVHP92] use this strategy. In the STS approach relatively short
substrings called probes are extracted from the DNA strand itself, often from the endpoints of clones. Each
probe is sufficiently long that it is highly unlikely to occur a second time on the DNA strand; thus it
identifies a unique site along the DNA strand. A probe is said to occur on a clone if it matches a substring

  

Source: Alizadeh, Farid - Rutgers Center for Operations Research, Rutgers University

 

Collections: Mathematics