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PubMed1992

Dynamic programming algorithms for restriction map comparison.

For most sequence comparison problems there is a corresponding map comparison algorithm. While map data may appear to be incompatible with dynamic programming, we show in this paper that the rigor and efficiency of dynamic programming algorithms carry over to the map comparison algorithms. We present algorithms for restriction map comparison that deal with two types of map errors: (i) closely spaced sites for different enzymes can be ordered incorrectly, and (ii) closely spaced sites for the same enzyme can be mapped as a single site. The new algorithms are a natural extension of a previous map comparison model. Dynamic programming algorithms for computing optimal global and local alignments under the new model are described. The new algorithms take about the same order of time as previous map comparison algorithms. Programs implementing some of the new algorithms are used to find similar regions within the Escherichia coli restriction map of Kohara et al.

Algorithms↗
PubMed1997

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.

We have developed a code generating language, called Dynamite, specialised for the production and subsequent manipulation of complex dynamic programming methods for biological sequence comparison. From a relatively simple text definition file Dynamite will produce a variety of implementations of a dynamic programming method, including database searches and linear space alignments. The speed of the generated code is comparable to hand written code, and the additional flexibility has proved invaluable in designing and testing new algorithms. An innovation is a flexible labelling system, which can be used to annotate the original sequences with biological information. We illustrate the Dynamite syntax and flexibility by showing definitions for dynamic programming routines (i) to align two protein sequences under the assumption that they are both poly-topic transmembrane proteins, with the simultaneous assignment of transmembrane helices and (ii) to align protein information to genomic DNA, allowing for introns and sequencing error.

Algorithms↗
PubMed1997

Automatic detection of cardiac contours on MR images using fuzzy logic and dynamic programming.

This paper deals with the use of fuzzy logic and dynamic programming in the detection of cardiac contours in MR Images. The definition of two parameters for each pixel allows the construction of the fuzzy set of the cardiac contour points. The first parameter takes into account the grey level, and the second the presence of an edge. A corresponding fuzzy matrix is derived from the initial image. Finally, a dynamic programming with graph searching is performed on this fuzzy matrix. The method has been tested on several MR images and the results of the contouring were validated by an expert in the domain. This preliminary work clearly demonstrates the interest of this method, although a formal evaluation has to be done.

Fuzzy Logic↗
PubMed1996

A segment-based dynamic programming algorithm for predicting gene structure.

An algorithm called segment-based dynamic programming is described for predicting gene structure from a sequence of genomic DNA. The algorithm explores the space of gene structures that satisfy junctional and frame constraints and finds the gene structure that optimizes the sum of junctional and segmental scoring functions. Junctional constraints specify acceptable sites of initiation, termination, and splicing, whereas frame constraints ensure that the total exon length is a multiple of three and that no in-frame stop codons occur within exons or at exon-exon junctions. By computing over segments, segment-based dynamic programming maintains reading frame and phase information for each segment, it can assemble exons in-frame as well as score them in-frame. The algorithm is used to quantify the computational power of constraints. Experimental results show that frame constraints reduce the size of the search space by several orders of magnitude and that cardinality constraints place an asymptotic limit on the size of the search space. The algorithm is also used to compare the accuracy of different methods for assembly and scoring. A scoring scheme based on fifth-order Markov hexamer frequencies is presented and used in three objective functions, corresponding to in-frame, frame-independent, and frame-maximal scoring strategies. Experimental results show that in-frame assembly improves specificity only slightly over frame-independent assembly, whereas in-frame scoring improves specificity substantially over frame-independent and frame-maximal scoring.

Algorithms↗
PubMed2001

A multithreaded parallel implementation of a dynamic programming algorithm for sequence comparison.

This paper discusses the issues involved in implementing a dynamic programming algorithm for biological sequence comparison on a general-purpose parallel computing platform based on a fine-grain event-driven multithreaded program execution model. Fine-grain multithreading permits efficient parallelism exploitation in this application both by taking advantage of asynchronous point-to-point synchronizations and communication with low overheads and by effectively tolerating latency through the overlapping of computation and communication. We have implemented our scheme on EARTH, a fine-grain event-driven multithreaded execution and architecture model which has been ported to a number of parallel machines with off-the-shelf processors. Our experimental results show that the dynamic programming algorithm can be efficiently implemented on EARTH systems with high performance (e.g., speedup of 90 on 120 nodes), good programmability and reasonable cost.

Algorithms↗
PubMed2000

Dynamic programming to investigate financial impacts of mastitis control decisions in milk production systems.

An adaptive stochastic dynamic programming model was used to solve the optimum replacement decision problem for the dairy cow under a range of alternative mastitis control procedures. The model predicted that reducing milk yield losses and somatic cell count penalties by, using milking machine test, post-milking teat disinfection and dry cow therapy added approximately pounds sterling 4, pounds sterling 10 and pounds sterling 13 respectively to an original annuity equivalent net present value for the replacement heifer of pounds sterling 286. Assuming that these procedures also reduced involuntary culling due to mastitis by 50% added pounds sterling 8.90 to the annuity. This latter figure indicated that an important part of the benefit of mastitis control procedures might come from a reduction in the culling risk of persistent clinical cases. We concluded that the strength of the dynamic programming model in this context was that it provided an integrated evaluation of the various impacts of each alternative mastitis procedure in the long term, which is essential for correct economic evaluation of mastitis.

Animals↗
PubMed1994

Considerations in applying dynamic programming filters to the smoothing of noisy data.

Dynamic programming techniques are useful in smoothing and differentiating noisy data signals according to an optimization criterion and the results are generally quite robust to noise spectra different from that assumed in the construction of the filter. If the noise properties are sufficiently different, however, the generalized cross-validation function used in the optimization can exhibit either multiple minima or no minima other than that corresponding to an insignificant amount of smoothing; in these cases, the smoothing parameter desired by the user typically does not lie at the global minimum of the generalized cross-validation function, but at some other point on the curve which can be identified heuristically. I present two cases to demonstrate this phenomenon and describe what measures one can take to ensure that the desired smoothing parameter is obtained.

Algorithms↗
PubMed2005

Fast unambiguous stereo matching using reliability-based dynamic programming.

An efficient unambiguous stereo matching technique is presented in this paper. Our main contribution is to introduce a new reliability measure to dynamic programming approaches in general. For stereo vision application, the reliability of a proposed match on a scanline is defined as the cost difference between the globally best disparity assignment that includes the match and the globally best assignment that does not include the match. A reliability-based dynamic programming algorithm is derived accordingly, which can selectively assign disparities to pixels when the corresponding reliabilities exceed a given threshold. The experimental results show that the new approach can produce dense (> 70 percent of the unoccluded pixels) and reliable (error rate < 0.5 percent) matches efficiently (< 0.2 sec on a 2GHz P4) for the four Middlebury stereo data sets.

Algorithms↗
PubMed1995

Recursive dynamic programming for adaptive sequence and structure alignment.

We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method. For this purpose, we consider the family of ferredoxins as our prime example. Our experiments show that, if properly tuned, the RDP method can outperform methods based on classical sequence alignment algorithms as well as methods that take purely structural information into account.

Amino Acid Sequence↗
PubMed2006

Automated contour detection in X-ray left ventricular angiograms using multiview active appearance models and dynamic programming.

This paper describes a new approach to the automated segmentation of X-ray left ventricular (LV) angiograms, based on active appearance models (AAMs) and dynamic programming. A coupling of shape and texture information between the end-diastolic (ED) and end-systolic (ES) frame was achieved by constructing a multiview AAM. Over-constraining of the model was compensated for by employing dynamic programming, integrating both intensity and motion features in the cost function. Two applications are compared: a semi-automatic method with manual model initialization, and a fully automatic algorithm. The first proved to be highly robust and accurate, demonstrating high clinical relevance. Based on experiments involving 70 patient data sets, the algorithm's success rate was 100% for ED and 99% for ES, with average unsigned border positioning errors of 0.68 mm for ED and 1.45 mm for ES. Calculated volumes were accurate and unbiased. The fully automatic algorithm, with intrinsically less user interaction was less robust, but showed a high potential, mostly due to a controlled gradient descent in updating the model parameters. The success rate of the fully automatic method was 91% for ED and 83% for ES, with average unsigned border positioning errors of 0.79 mm for ED and 1.55 mm for ES.

Algorithms↗
PubMed2006

Time continuous tracking and segmentation of cardiovascular magnetic resonance images using multidimensional dynamic programming.

In this article, we propose a semiautomatic method for time-continuous contour detection in all phases of the cardiac cycle in magnetic resonance sequences. The method is based on multidimensional dynamic programming. After shape parameterization, cost hypercubes are filled with image-feature derived cost function values. Using multidimensional dynamic programming, an optimal path is sought through the sequence of hypercubes. Constraints can be imposed by setting limits to the parameter changes between subsequent hypercubes. Quantitative evaluation was performed on 20 subjects. Average border positioning error over all slices, all phases and all studies, was 1.77 +/- 0.57 mm for epicardial and 1.86 +/- 0.59 mm for endocardial contours. The average error in end-diastolic and end-systolic volumes over all studies was small: 4.24 +/- 4.62 mL and -4.36 +/- 4.26 mL, respectively. The average error in ejection fraction was 4.82 +/- 3.01%. The reported results compare favorable to the best-reported results in recent literature, underlining the potential of this method for application in daily clinical practice.

Algorithms↗
PubMed2004

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.

A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs.

Algorithms↗
PubMed2002

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.

BACKGROUND: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs. RESULTS: I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N) memory complexity, at the expense of a small constant factor in time. CONCLUSIONS: Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.

Algorithms↗
PubMed2005

An adaptive dynamic programming algorithm for the side chain placement problem.

Larger rotamer libraries, which provide a fine grained discretization of side chain conformation space by sampling near the canonical rotamers, allow protein designers to find better conformations, but slow down the algorithms that search for them. We present a dynamic programming solution to the side chain placement problem which treats rotamers at high or low resolution only as necessary. Dynamic programming is an exact technique; we turn it into an approximation, but can still analyze the error that can be introduced. We have used our algorithm to redesign the surface residues of ubiquitin's beta sheet.

Algorithms↗
PubMed1998

Dynamic programming alignment accuracy.

Algorithms for generating alignments of biological sequences have inherent statistical limitations when it comes to the accuracy of the alignments they produce. Using simulations, we measure the accuracy of the standard global dynamic programming method and show that it can be reasonably well modelled by an "edge wander" approximation to the distribution of the optimal scoring path around the correct path in the vicinity of a gap. We also give a table from which accuracy values can be predicted for commonly used scoring schemes and sequence divergences (the PAM and BLOSUM series). Finally we describe how to calculate the expected accuracy of a given alignment, and show how this can be used to construct an optimal accuracy alignment algorithm which generates significantly more accurate alignments than standard dynamic programming methods in simulated experiments.

Algorithms↗
PubMed1990

Determining minimum energy conformations of polypeptides by dynamic programming.

A combinatorial optimization approach is used for solving the multiple-minima problem when determining the low-energy conformations of short polypeptides. Each residue is represented by a finite number of discrete states corresponding to single residue local minima of the energy function. These precomputed values constitute a search table and define the conformational space for discrete minimization by a generalized dynamic programming algorithm that significantly limits the number of intermediate conformations to be generated during the search. Since dynamic programming involves stagewise decisions, it results in buildup-type procedures implemented in two different forms. The first procedure predicts a number of conformations by a completely discrete search and these are subsequently refined by local minimization. The second involves limited continuous local minimization within the combinatorial algorithm, generally restricted to two dihedral angles in a buildup step. Both procedures are tested on 17 short peptides previously studied by other global minimization methods but involving the same potential energy function. The discrete method is extremely fast, but proves to be successful only in 14 of the 17 test problems. The version with limited local minimization finds, however, conformations in all the 17 examples that are close to the ones previously presented in the literature or have lower energies. In addition, results are almost independent of the cutoff energy, the most important parameter governing the search. Although the limited local minimization increases the number of energy evaluations, the method still offers substantial advantages in speed.

Algorithms↗
PubMed2004

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.

UNLABELLED: Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed with regions of low LD. Such LD patterns make it possible to select a set of single nucleotide polymorphism (SNPs; tag SNPs) for genome-wide association studies. We have developed a suite of computer programs to analyze the block-like LD patterns and to select the corresponding tag SNPs. Compared to other programs for haplotype block partitioning and tag SNP selection, our program has several notable features. First, the dynamic programming algorithms implemented are guaranteed to find the block partition with minimum number of tag SNPs for the given criteria of blocks and tag SNPs. Second, both haplotype data and genotype data from unrelated individuals and/or from general pedigrees can be analyzed. Third, several existing measures/criteria for haplotype block partitioning and tag SNP selection have been implemented in the program. Finally, the programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs. AVAILABILITY: The HapBlock program and its supplemental documents can be downloaded from the website http://www.cmb.usc.edu/~msms/HapBlock.

Algorithms↗
PubMed1990

Alignment of protein sequences using secondary structure: a modified dynamic programming method.

A method for comparison of protein sequences based on their primary and secondary structure is described. Protein sequences are annotated with predicted secondary structures (using a modified Chou and Fasman method). Two lettered code sequences are generated (Xx, where X is the amino acid and x is its annotated secondary structure). Sequences are compared with a dynamic programming method (STRALIGN) that includes a similarity matrix for both the amino acids and secondary structures. The similarity value for each paired two-lettered code is a linear combination of similarity values for the paired amino acids and their annotated secondary structures. The method has been applied to eight globin proteins (28 pairs) for which the X-ray structure is known. For protein pairs with high primary sequence similarity (greater than 45%), STRALIGN alignment is identical to that obtained by a dynamic programming method using only primary sequence information. However, alignment of protein pairs with lower primary sequence similarity improves significantly with the addition of secondary structure annotation. Alignment of the pair with the least primary sequence similarity of 16% was improved from 0 to 37% 'correct' alignment using this method. In addition, STRALIGN was successfully applied to seven pairs of distantly related cytochrome c proteins, and three pairs of distantly related picornavirus proteins.

Amino Acid Sequence↗