@inproceedings{3d23ca1ea579440da0075a4686eef940,
title = "Fast optimal genome tiling with applications to microarray design and homology search",
abstract = "In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we discuss the solution of a basic online interval maximum problem via a sliding window approach and show how to use this solution in a nontrivial manner for many of our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.",
author = "Piotr Berman and Paul Bertone and Bhaskar DasGupta and Mark Gerstein and Ming-Yang Kao and Michael Snyder",
note = "Publisher Copyright: {\textcopyright} Springer-Verlag Berlin Heidelberg 2002.; 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 ; Conference date: 17-09-2002 Through 21-09-2002",
year = "2002",
doi = "10.1007/3-540-45784-4_32",
language = "English (US)",
isbn = "3540442111",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "419--433",
editor = "Roderic Guigo and Dan Gusfield",
booktitle = "Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings",
}