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T h e h is tory and mot iva t ion Although I d idn ' t know it at the time, I began writing this book in the summer of 1988 when I was part of a computer science research group at the Human Genome Center of Lawrence Berkeley Laboratory. Our group followed the standard assumption that biologically meaningful results could come from considering DNA as a(More)
Linear-Time Construction of Suffix Trees We will present two methods for constructing suffix trees in detail, Ukkonen’s method and Weiner’s method. Weiner was the first to show that suffix trees can be built in linear time, and his method is presented both for its historical importance and for some different technical ideas that it contains. However,(More)
Where you can find the the stable marriage problem structure and algorithms easily? Is it in the book store? On-line book store? are you sure? Keep in mind that you will find the book in this site. This book is very referred for you because it gives not only the experience but also lesson. The lessons are very valuable to serve for you, that's not about who(More)
Partitioning of a set of elements into disjoint clusters is a fundamental problem that arises in many applications. Different methods produce different partitions, so it is useful to have a measure of the similarity, or distance, between two or more partitions. In this paper we examine one distance measure used in a clustering application in computational(More)
A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. With the growth of genomic data, much of which does not fit ideal tree models, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks [10, 11]. However, to date, very little has been published on(More)
A full haplotype map of the human genome will prove extremely valuable as it will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A haplotype map project has been announced by NIH. The biological key to that project is the surprising fact that some human genomic DNA can be(More)
We study the problem of detecting all occurrences of (primitive) tandem repeats and tandem arrays in a string. We first give a simple timeand space-optimal algorithm to find all tandem repeats, and then modify it to become a time and space-optimal algorithm for finding only the primitive tandem repeats. Both of these algorithms are then extended to handle(More)