On physical mapping algorithms - an error tolerant test for the consecutive ones property

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On Physical Mapping Algorithms -- An Error-Tolerant Test for the Consecutive Ones Property

An important problem in physical mapping is to test the consecutive ones property of a (0,1)-matrix: that is, whether it is possible to permute the columns so that each row of the resulting matrix has the ones occur in a consecutive block. This is useful, for example, in probe hybridization for cosmid clones and in the STS content mapping of YAC library. The linear time algorithm by Booth and Lueker (1975) for this problem has a serious drawback: the data must be error-free. However, laboratory work is never flawless. We devised a new algorithm for this problem, which has the following advantages: 1. conceptually, it is very simple; 2. it produces a matrix satisfying the consecutive ones property in linear time when the matrix satisfies the consecutive ones property; 3. with reasonable assumptions, it can accommodate the following three types of errors in physical mapping: false negatives, false positives and chimeric clones; 4. in the rare case that the assumptions in 3 are not satisf..

Propriedade dos uns consecutivos e arvores PQR

Orientador: João MeidanisDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Neste trabalho formalizamos as Árvores PQR de Meidanis e Munuera e seu relacionamento com a propriedade dos uns consecutivos e com as Árvores PQ de Booth e Lueker. Mostramos que uma árvore PQR construída para uma coleção C de subconjuntos de um universo U é capaz de armazenar todas as permutações de U que verificam a propriedade dos uns consecutivos. Apresentamos dois algoritmos para construir as árvores PQR, um recursivo e outro não recursivo, e alguns problemas relativos à propriedade e às coleções de conjuntos que podem ser resolvidos através destas árvores. Analisamos, ainda, um conjunto de aplicações das Árvores PQ e consideramos a possibilidade de empregar as árvores PQRAbstract: In the present work we formalize Meidanis and Munuera's PQR trees and their relationship with the Consecutive Ones Property and with Booth and Lueker's PQ trees. We show that a PQR tree built for a colIection C of subsets of a ground set U is able to store alI permutations of U that verify the consecutive ones property. We introduce two algorithms that build the PQR trees, a recursive and a non recursive one, and some problems related to the consecutive ones property and to colIections of sets that can be solved using them. We analyze some applications of the PQ trees and inspect the useness of the PQR treesMestradoMestre em Ciência da Computaçã