Space and time optimal parallel sequence alignments
نویسندگان
چکیده
منابع مشابه
Optimal alignments in linear space
Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it...
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The growth of bioinformatics and computational biology industry, multiple sequence alignment (MSA) applications have become an important emerging workload. In spite of the large amount of recent attention given to the MSA software design, there has been little quantitative understanding of the performance of such applications on modern microprocessors and systems. In this paper we try to analyz...
متن کاملVisualization of near-optimal sequence alignments
MOTIVATION Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful a...
متن کاملOptimal Alignment of Multiple Sequence Alignments
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 CHAPTER 1: INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . 14 1.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 1.2 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 1.3 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...
متن کاملCyclic Sequence Alignments: Approximate Versus Optimal Techniques
The problem of cyclic sequence alignment is considered. Most existing optimal methods for comparing cyclic sequences are very time consuming. For applications where these alignments are intensively used, optimal methods are seldom a feasible choice. The alternative to an exact and costly solution is to use a close-to-optimal but cheaper approach. In previous works, we have presented three subop...
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ژورنال
عنوان ژورنال: IEEE Transactions on Parallel and Distributed Systems
سال: 2004
ISSN: 1045-9219
DOI: 10.1109/tpds.2004.86