E. Birney and R. Durbin. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. Proc. Fifth Int. Conf. Intelligent Systems Mol. Biol. 5:55-64 (1997).  Home/Search   Document Details and Download   Summary   Related Articles   Check

....(Durbin et al. 1998) presents a dozen variants of DP algorithms in its introductory chapter on sequence comparison. In some areas of computational biology, dynamic programming problems arise in such variety that a specific code generation system for implementing such algorithms has been developed (Birney and Durbin, 1997). 1.2 Some of the Intrinsic Difficulties of Dynamic Programming Algorithms The development of a DP algorithm is a challenging task. The core of the algorithm is given by a set of recurrences, defin1 Systematic Dynamic Programming 2 ing the entries in one or more matrices. Neither the ....

....with their own terminology, living in happy ignorance of the Chomksy hierarchy (Durbin et al. 1998) The regular case in ADP is a yield grammar that makes no use of the and the operator; beyond this, it requires no special treatment to reach O(n 2 ) time efficiency. The Dynamite system (Birney and Durbin, 1997) provides a code generation language for dynamic programming recurrences, while our approach is concerned with their development. Although the system can be of great benefit to the expert, it has not (yet) found the widespread use one might expect. One reason certainly is that the development of ....

Birney, E. and Durbin, R. (1997). Dynamite: A flexible code generating language for dynamic programming methods, Proc. Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, USA, pp. 56--64.

....[1] RNA folding [24, 39] structure comparison [32] gene recognition [8, 34] and a multitude of further applications. For a recent overview of basic and advanced techniques, see [2] and therein [9] In some research contexts, a large number of such programs must be developed; the Dynamite system [5] has been designed to support the implementation of sequence comparison algorithms based on dynamic programming. The present article is devoted to the problem of developing DP algorithms in the area of RNA secondary structure determination. 1.2 Sketch of results We show how the development of ....

....construction community; in our opinion, they are still too low level a formalism to be useful as a program development methodology in bioinformatics. By contrast, all the parsing technology required by our approach is completely described in a small section of this article. The Dynamite system [5] provides a code generation language for dynamic programming recurrencies, while our approach is concerned with their development. Although the system can be of great benefit to the expert, it has not (yet) found the widespread use one might expect. One reason certainly is that the development of ....

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E. Birney and R. Durbin. Dynamite: A flexible code generating language for dynamic programming methods. In 5th International Conference on Intelligent Systems for Molecular Biology, pages 56--64, 1997.

....grammar. His genefinding program, GenLang, was one of the earliest integrated genefinders, following on the pioneering work of Gelfand [26] Gelfand and Roytberg [30] Fields and Soderlund [24] and Phil Green s GeneFinder[69] and was one of the inspirations for significant later work (e.g. [6, 5] and the HMM methods described below. Nearly all integrated genefinders use dynamic programming to combine candidate exons and other scored regions and sites into an complete gene prediction with maximal total score. A brief and lucid tutorial on this topic can be found in [41] and a more ....

....the case that homologs are unknown or are remote, in which case this system would be inappropriate. Nevertheless, in the presence of a very close homolog, Procrustes is an extremely effective gene finding method. Recent related methods, based on HMM models, have been developed by Birney and Durbin [5] and are currently being developed by Kulp [43] In 1995, a number of different integrated genefinders were tested on a benchmark set of 570 vertebrate genes by Burset and Guig o [10] They looked at not only how many bases were predicted correctly as either coding or non coding, but how many ....

E. Birney and R. Durbin. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. In ismb97, pages 56--64, 1997.

.... the use of the Baum Welch algorithm for finding the optimal scoring scheme [Kro94, HK96] The probabilistic formulation has been extended to pairwise alignment [BH96, ZLL98] and it has also been widely used for gene prediction (see [Hau98] for a review) as well as more eclectic HMM architectures [BD97] The connection to Bayesian machine learning research continues to generate interesting new ideas such as probability density networks [Mac96a, Pov98] and Fisher kernels [JH98] With this context, Part I of this thesis can be summarised. 1.2.2 Summary of Part I of the thesis Part I of this ....

....is anticipated that there will also be pseudogene containing variants with internal deletions or insertions [OGB96] For these reasons the blastx program, which searches the six frame conceptual translation of the genomic sequence, may not be sensitive enough. A more sensitive program is GeneWise [BD97] which finds the optimal alignment of conceptually translated genomic sequence to a hidden Markov model (HMM) and is robust to gaps and frameshifts. HMMs were trained individually on three separate seed alignments: the first produced using CLUSTALW [THG94a] from all the mariner transposases in ....

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E. Birney and R. Durbin. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. In Gaasterland et al. [GKK + 97], pages 56--64.

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E. Birney and R. Durbin. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. Proc. Fifth Int. Conf. Intelligent Systems Mol. Biol. 5:55-64 (1997).

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Birney,E. and Durbin,R. (1997) Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. In Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology, 5, 56--64. AAAI Press, Menlo Park.

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