Blanchette,M. (2001) Algorithms for phylogenetic footprinting. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01). Montr eal, Canada.  Home/Search   Document Details and Download   Summary   Related Articles   Check

.... proofs can be found in the techreport at (monod.uwaterloo.ca mhu hyper hyper.ps) 1 Introduction Inferring phylogenetic trees on molecular sequences has wide applications in biology, from analyzing the evolutionary history of AIDS [8] to detecting regulatory elements in genetic sequences [1]. The problem of phylogenetic inference is considered hard from both a biological and computational perspective. However many biologists believe that maximum likelihood (ML) based methods are the best vehicle for conducting phylogenetic analysis [9] 14] ML methods are, however, NP hard ....

Blanchette, M. Algorithms for phylogenetic footprinting. In Proceedings of the 5th Conference on Research in Computational Molecular Biology (2001), ACM Press, pp. 49-58.

....solving NP hard problems can be completely restricted to the parameter l. Note, however, that for LCS this requires that is of constant size. If is unbounded, then there is concrete indication that LCS is not fixed parameter tractable with respect to parameter l (by way of socalled W[2] hardness which is well known in parameterized complexity) We Actually, in case of LCS running time O( # N) is easily achieved. refer to [3,4,6,23] for any details. Evans [7,8] initiated classical and parameterized complexity studies for the more general case that the input sequences ....

....less than all theoretically possible candidate patterns) should enable significant accelerations of the above algorithm in applications. A good example of the practical success of such an enumerative approach in computational molecular biology is the recent result of Blanchette et al. [2] in the context of motif search for DNA sequences. 4 Search Tree Algorithm for LAPCS(nested,nested) In this section, we describe and analyze Algorithm STA which solves the LAPCS(nested, nested) problem in O(3.31 n) time, where n is the maximum length of the input sequences, and k 1 and k 2 ....

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M. Blanchette, B. Schwikowski, and M. Tompa. Algorithms for phylogenetic footprinting. Journal of Computational Biology, 9(2):211--224, 2002.

.... proofs can be found in the techreport at (monod.uwaterloo.ca mhu hyper hyper.ps) 1 Introduction Inferring phylogenetic trees on molecular sequences has wide applications in biology, from analyzing the evolutionary history of AIDS [8] to detecting regulatory elements in genetic sequences [1]. The problem of phylogenetic inference is considered hard from both a biological and computational perspective. However many biologists believe that maximum likelihood (ML) based methods are the best vehicle for conducting phylogenetic analysis [9] 14] ML methods are, however, NP hard ....

Blanchette, M. Algorithms for phylogenetic footprinting. In Proceedings of the 5th Conference on Research in Computational Molecular Biology (2001), ACM Press, pp. 49-58.

.... in genomics and proteomics: Database search methods for homologous sequences, can be made more e#cient using an evolutionary tree as a guide [42] Detecting potential gene expression regulatory elements by finding conserved regions in a set of orthologous, non coding DNA sequences [5], requires accurate phylogenetic information. Phylogenetic analysis can provide valuable metrics for governing gene function prediction algorithms. 39, 13] Evolutionary trees can be used as valuable roadmaps for inferring gene duplication events in genomes [14] 9] inferring gene ....

Blanchette, M. Algorithms for phylogenetic footprinting. In Proceedings of the 5th Conference on Research in Computational Molecular Biology (2001), ACM Press, pp. 49--58.

....tools for the scientific community. Many new research directions are currently being pursued in this area; for example, pair wise sequence comparisons can be expanded to include multiple species and to make use of additional information, such as evolutionary distance and phylogenetic relationships [25]. More precise and effective sequence alignment programs have been created to handle genome scale sequences [26,27] In addition to the human mouse comparisons, some researchers are also proposing cross species comparison between human and other primates, which has been described as phylogenetic ....

Blanchette M, Schwikowski B, Tompa M: Algorithms for phylogenetic footprinting. J Comput Biol 2002, 9:211-223.

....Wilhelm Schickard Institut f ur Informatik, Universit at T ubingen, Sand 13, D 72076 T ubingen, Fed. Rep. of Germany fgramm, niedermrg informatik.uni tuebingen.de Abstract. We show that Closest Substring, one of the most important problems in the eld of biological sequence analysis, is W[1] hard with respect to the number k of input strings (even over a binary alphabet) This problem is therefore unlikely to be solvable in time O(f(k)n for any function f and constant c independent of k e ectively, the problem can be expected to be intractable, in any practical sense, for k ....

....to be intractable, in any practical sense, for k 3. Our result supports the intuition that Closest Substring is computationally much harder than the special case of Closest String, although both problems are NP complete and both possess polynomial time approximation schemes. We also prove W[1] hardness for other parameterizations in the case of unbounded alphabet size. Our main W[1] hardness result generalizes to Consensus Patterns, a problem of similar signi cance in computational biology. 1 Introduction According to Li et al. 11] Closest Substring is a key open problem in ....

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M. Blanchette. Algorithms for phylogenetic footprinting. In Proc. of 5th ACM RECOMB , pages 49-58, 2001, ACM Press.

....it to nd known transcriptional regulatory elements upstream of several eukaryotic genes. We examined orthologous sequences from a variety of organisms taken from regions upstream of four types of gene: preproinsulin, dihydrofolate reductase (DHFR) metallothioneins, and c fos. See Blanchette [3] for an alternative approach to nding motifs in these sequences. These sequences are known to contain binding sites for speci c transcription factors. We also tested a collection of promoter regions 1 from the yeast S. cerevisiae that is known to contain a shared cell cycle dependent promoter ....

....were usually slightly shifted windows covering the same underlying site. For these experiments, we report only the most 5 0 shifted consensus string. Although the motifs we found are not particularly subtle, and indeed have previously been found by standard iterative methods such as MEME [3], the results of these experiments are noteworthy for two reasons. First, we achieved good performance even with a fairly primitive re nement strategy that did not include, e.g. motif length corrections, information based scoring, or iteration of EM to convergence. We expect that random ....

M. Blanchette. Algorithms for phylogenetic footprinting. In RECOMB01: Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, Montreal, Canada, Apr. 2001.

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Blanchette,M. (2001) Algorithms for phylogenetic footprinting. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01). Montr eal, Canada.

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M. Blanchette, B. Schwikowski, and M. Tompa. Algorithms for phylogenetic footprinting. Journal of Computational Biology, 9(2):211--224, 2002.

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Blanchette, M., Schwikowski, B., and Tompa, M., Algorithms for phylogenetic footprinting, J. Comput. Biol., 9(2):211--223, 2002.

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M. Blanchette, B. Schwikowski, and M. Tompa. Algorithms for phylogenetic footprinting. J. Comput. Bio., 9(2):211223, 2002.

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M. Blanchette, B. Schwikowski, and M. Tompa. Algorithms for phylogenetic footprinting. Journal of Computational Biology, 9(2):211--224, 2002.

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Blanchette, M. Algorithms for phylogenetic footprinting. In Proceedings of the 5th Conference on Research in Computational Molecular Biology (2001), ACM Press, pp. 49--58.

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Blanchette, M. Algorithms for phylogenetic footprinting. In Proceedings of the 5th Conference on Research in Computational Molecular Biology (2001), ACM Press, pp. 49-58.

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