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Combinatorial algorithms for DNA sequence assembly
 Algorithmica
, 1993
"... The trend towards very large DNA sequencing projects, such as those being undertaken as part of the human genome initiative, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The seq ..."
Abstract

Cited by 43 (3 self)
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The trend towards very large DNA sequencing projects, such as those being undertaken as part of the human genome initiative, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of DNA sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing errors and reverse complements of fragments. Since the simpler superstring problem is NPhard, any efficient reconstruction procedure must resort to heuristics. In this paper, however, a four phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice. Our method is robust in the sense that it can accommodate high sequencing error rates and list a series of alternate solutions in the event that several appear equally good. Moreover it uses a limited form ...
AMASS: A Structured Pattern Matching Approach to Shotgun Sequence Assembly
 J. Comput. Biol
, 1999
"... In this paper, we propose an efficient, reliable shotgun sequence assembly algorithm based on a fingerprinting scheme that is robust to both noise and repetitive sequences in the data. Our algorithm uses exact matches of short patterns randomly selected from fragment data to identify fragment overla ..."
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Cited by 15 (3 self)
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In this paper, we propose an efficient, reliable shotgun sequence assembly algorithm based on a fingerprinting scheme that is robust to both noise and repetitive sequences in the data. Our algorithm uses exact matches of short patterns randomly selected from fragment data to identify fragment overlaps, construct an overlap map, and finally deliver a consensus sequence. We show how statistical clues made explicit in our approach can easily be exploited to correctly assemble results even in the presence of extensive repetitive sequences. Our approach is exceptionally fast in practice: e.g., we have successfully assembled a whole Mycoplasma genitalium genome (approximately 580 kbps) in roughly 8 minutes of 64MB 200MHz Pentium Pro CPU time from real shotgun data, where most existing algorithms can be expected to run for several hours to a day on the same data. Moreover, experiments with shotgun data synthetically prepared from real DNA sequences from a wide range of organisms (including h...
New generations: Sequencing machines and their computational challenges
 Journal of Computer Science and Technology
"... Abstract New generation sequencing systems are changing how molecular biology is practiced. The widely promoted 1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations w ..."
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Cited by 2 (0 self)
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Abstract New generation sequencing systems are changing how molecular biology is practiced. The widely promoted 1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations will be commonplace. What is less appreciated is the explosive demands on computation, both for CPU cycles and storage as well as the need for new computational methods. In this article we will survey some of these developments and demands. Keywords graphs
Approximation Algorithms For The Shortest
 Information and Computation
, 1989
"... The object of the shortest common superstring problem (SCS) is to find the shortest possible string that contains every string in a given set as substrings. As the problem is NPcomplete, approximation algorithms are of interest. The value of an approximate solution to SCS is normally taken to be it ..."
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The object of the shortest common superstring problem (SCS) is to find the shortest possible string that contains every string in a given set as substrings. As the problem is NPcomplete, approximation algorithms are of interest. The value of an approximate solution to SCS is normally taken to be its length, and we seek algorithms that make the length as small as possible. A different measure is given by the sum of the overlaps between consecutive strings in a candidate solution. When considering this measure, the object is to find solutions that make it as large as possible. These two measures offer different ways of viewing the problem. While the two viewpoints are equivalent with respect to optimal solutions, they differ with respect to approximate solutions. We describe several approximation algorithms that produce solutions that are always within a factor of two of optimum with respect to the overlap measure. We also describe an efficient implementation of one of these, using McCreight's compact suffix tree construction algorithm. The worstcase running time is O(m log n) for small alphabets, where m is the sum of the lengths of all the strings in the set and n is the number of strings. For large alphabets, the algorithm can be implemented in O(m log m) time by using Sleator and Tarjan's lexicographic splay tree data structure.