Linear Time Algorithms for Computing Maximum Density Sequence…用于计算最大密度序列的线性时间算法.pdfVIP

Linear-Time Algorithms for Computing Maximum-Density Sequence Segments with Bioinformatics Applications Michael H. Goldwasser Department of Mathematics and Computer Science Saint Louis University 221 N. Grand Blvd St. Louis, MO 63103-2007 Email: goldwamh@ URL: /˜goldwasser Ming-Yang Kao 1 Department of Computer Science Northwestern University Evanston, IL 60201. Email: kao@ URL: /˜kao Hsueh-I Lu 2 Institute of Information Science Academia Sinica 128 Academia Road, Section 2 Taipei 115, Taiwan. Email: hil@.tw URL: .tw/˜hil A preliminary version of these results appeared under the title, “Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioin- formatics,” in Proceedings of the Second Workshop on Algorithms in Bioinformat- ics (WABI), volume 2452 of Lecture Notes in Computer Science (Springer-Verlag, Berlin), R. Guig´o and D. Gusfield editors, 2002, pp. 157–171. 1 Supported in part by NSF grant EIA-0112934. 2 Supported in part by NSC grant NSC-90-2218-E-001-005. Preprint submitted to Elsevier Science 3 August 2004 Abstract We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a , w ) for i = 1, . . . , n and w 0, a seg-