Algorithms On Strings Trees And Sequences By Dan Gusfield PdfBy Claudette F. In and pdf 21.04.2021 at 15:18 9 min read
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Jetzt bewerten Jetzt bewerten. String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data DNA or protein sequences produced by various genome projects.
- Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology
- Dan Gusfield
- Algorithms on Strings, Trees, and Sequences (eBook, PDF)
Gusfield Cambridge Press.
Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology
Gusfield Cambridge Press. Gusfield and R. Irving MIT Press. The paper uses approximation algorithms in a way that is backwards from what they were designed for, in order to establish bounds on the accuracy of certain computations, rather than trying to find good solutions.
The key to doing this is to make an approximation algorithm as inaccurate as possible, while still producing a solution that falls within the worst-case approximation bound. We use this approach to try to show that a particular tree alignment of RNA sequences that David Sankoff and Robert Cedergren constructed in is close to the optimal alignment under a given objective function.
In this paper we show that its cost is no more than I think this idea of using an approximation algorithm backwards can be applied in other problems, but I have never seen the idea picked up by anyone else. This was the first use of a bounded approximation algorithm in computational biology. The particular multiple alignment method developed in the paper was only for the purpose of being able to prove a guaranteed bound on the error, and hence the result in the paper is mainly theoretical.
However, it has been reported that the actual alignments are useful in some applications. A historical trivia note: This is the first oldest paper PubMed indexed using the search term Computational Biology. Gusfield and P. StellingMethods in Enzymology, Vol. Return to Gusfield Homepage April, Gysel and D. Gusfield and Y. Gusfield, S. The main result of the paper is that there is a three-state perfect phylogeny or in other terms, the data is compatible with a three-state tree if and only if there is one for every subset of three characters.
This generalizes the binary case where the classical four-gametes condition says that there is a binary perfect phylogeny in binary data if and only if there is one for every pair of characters. The paper also shows that there is a set of four subpatterns, each with three characters and five taxa, such that any three-state data that does not have a three-state perfect phylogeny must contain one of those four subpatterns.
This generalizes the four-gametes condition which shows that when a pair of characters does not have a binary perfect phylogeny is not compatible the subpattern of all four binary combinations must appear in that pair of characters.
The techniques are based on the chordal graph view of perfect phylogeny. Expanded journal version with complete proofs J. It solves the major open question from that conference paper and extends the earlier results. A new recombination lower bound and the minimum perfect phylogenetic forest problem Y.
Wu and D. Gusfield LNCS, vol. Gusfield, D. Hickerson, S. The journal version appeared in J. Bioinformatics and Computational Biology, Vol. Song, Z. Ding, D. Gusfield, C. Langley, Y. Gusfield and V. Gusfield November 25, , Journal version appears in J. Eddhu, C. This is a much expanded journal version of the conference paper listed next. This won the best-paper award. Thank you Hewlett Packard for donating the prize money.
Orzack, D. Gusfield, L. Subrahmanyan, L. Essioux, S. Mandoiu and A. Zelikovsky eds. Song, Y. Wu and Gusfield Proceedings of WABI , October , Lecture Notes in Bioinformatics In this paper we look at extensions of the PPH problem see below to situations where the underlying haplotypes that form the genotypes do not evolve on a perfect phylogeny, but rather evolve either on a tree with one homoplasy event a recurrent or back mutation or on a network with one recombination event.
Using one emprically-justified assumption, we present a polynomial time algorithm for the first problem the case of one homoplasy event and an exponential-time algorithm for the second problem. We have subsequently developed a polynomial-time algorithm for the second problem as well. Ding, V. Filkov, D. Journal of Computational Biology, Vol. The method presented is simple enough for easy implementation, and our implementation is on the web.
Haplotype Inference pdf D. Gusfield and S. Aluru Editor , p. Istrail, M. W aterman, and A. Clark eds. Lecture Notes in Computer Science, vol. Chung and D. Gusfield Proceedings of the Cocoon Conference July Link to the proceedings This reports on the performance of three perfect phylogeny haplotyping programs, and on two interesting phenomena observed when solving the perfect phylogeny haplotyping problem on simulated data.
Gusfield January 23, , Final version in The Proceedings of the Combinatorial Pattern Matching Conference, June Link to conference proceedings The Pure Parsimony problem for Haplotype Inference is to find the smallest set of binary strings that can generate an input set of genotypes. The Pure Parsimony problem is NP-hard, and no paper has previously shown how an optimal Pure-Parsimony solution can be computed efficiently for problem instances of the size of current biological interest.
In this paper, we show how to formulate the Pure-Parsimony problem as an integer linear program; we explain how to improve the practicality of the integer programming formulation; and we present the results of extensive experimentation we have done to show the time and memory practicality of the method, and to compare its accuracy against solutions found by the widely used general haplotyping program PHASE.
The results are that the Pure Parsimony problem can be solved efficiently in practice for a wide range of problem instances of current interest in biology. Both the time needed for a solution, and the accuracy of the solution, depend on the level of recombination in the input strings.
The speed of the solution improves with increasing recombination, but the accuracy of the solution decreases with increasing recombination. Haplotyping as Perfect Phylogeny: A direct approach pdf. Bafna, D. Gusfield, G.
Lancia, S. Yooseph July 17, An augmented version has appeared in Journal of Computational Biology, Vol. It gives a more intuitive and algorithmicly simpler way to create the representation of all such solutions. An implementation of this method is available at: DPPH. This paper develops an almost-linear-time algorithm to determine if unphased genotype data can be explained by haplotype pairs which fit a rooted perfect phylogeny.
If there is such an explanation, then the algorithm, in linear additional time, determines if the solution is unique, and if not, produces a representation of all the solutions. The method is based on reducing the haplotype problem to a problem of graph realization. However, in GPPH, we use a somewhat slower way to solve the graph realization problem than is described in the paper.
Bioinformatics, Vol. Gusfield, V. This paper is almost unique in the literature in that it compares the accuracy of the methods to laboratory determined haplotype data — determined by one of the authors. It is the joint collaboration of a computer scientist, a geneticist and molecular biologists. Stanton, Jr.
Frid and D. Brown LNCS, vol. Gusfield and J. Stoye JCSS, vol. The algorithm runs in linear-time as a function of the length of the string. Of course, such an algorithmic result would not be possible without the remarkable mathematical result, proven by A. Frankel and J. Simpson in , that there can only be a linear number of distinct substrings that are tandem repeats. The actual bound is 2n, for a string of length n. After the suffix tree is decorated, almost all imaginable questions about the tandem repeats or tandem arrays how many occurrences there are, where they occurr, their average length, the maximum and minimum lengths from given positions etc.
Gusfield Program Chair , P.
String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data DNA or protein sequences produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone.
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Algorithms on Strings, Trees, and Sequences (eBook, PDF)
Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Gusfield Published Computer Science. Part I.
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