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Efficient Methods for Determining DNA Probe Orders
Hiro ITO Kazuo IWAMA Takeyuki TAMURA
Publication
IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences
Vol.E89A
No.5
pp.12921298 Publication Date: 2006/05/01 Online ISSN: 17451337
DOI: 10.1093/ietfec/e89a.5.1292 Print ISSN: 09168508 Type of Manuscript: Special Section PAPER (Special Section on Discrete Mathematics and Its Applications) Category: Keyword: DNA, hybridization, probe, fragment, PQtree,
Full Text: PDF(320.7KB)>>
Summary:
In STSbased mapping, it is necessary to obtain the correct order of probes in a DNA sequence from a given set of fragments or an equivalently a hybridization matrix A. It is wellknown that the problem is formulated as the combinatorial problem of obtaining a permutation of A's columns so that the resulting matrix has a consecutiveone property. If the data (the hybridization matrix) is error free and includes enough information, then the above column order uniquely determines the correct order of the probes. Unfortunately this does not hold if the data include errors, and this has been a popular research target in computational biology. Even if there is no error, ambiguities in the probe order may still remain. This in fact happens because of the lack of some information regarding the data, but almost no further investigation has previously been made. In this paper, we define a measure of such imperfectness of the data as the minimum amount of the additional fragments that are needed to uniquely fix the probe order. Polynomialtime algorithms to compute such additional fragments of the minimum cost are presented. A computer simulation using genes of human chromosome 20 is also noted.

