16612931
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution
MOTIVATION
We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NP-hard, and previous algorithms that compute it exactly work either only on very small datasets or on problems with special structure.


RESULTS
In this paper, we present efficient, practical methods for computing both upper and lower bounds on the minimum number of needed recombinations, and for constructing evolutionary histories that explain the input sequences. We study in detail the efficiency and accuracy of these algorithms on both simulated and real data sets. The algorithms produce very close upper and lower bounds, which match exactly in a surprisingly wide range of data. Thus, with the use of new, very effective lower bounding methods and an efficient algorithm for computing upper bounds, this approach allows the efficient, exact computation of the minimum number of needed recombinations, with high frequency in a large range of data. When upper and lower bounds match, evolutionary histories found by our algorithm correspond to the most parsimonious histories.


AVAILABILITY
HapBound and SHRUB, programs implementing the new algorithms discussed in this paper, are available at http://wwwcsif.cs.ucdavis.edu/~gusfield/lu.html
40339335
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations
Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is “association mapping” in populations, which is widely hoped to help find genes that influence genetic diseases [3, 4]. Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to single-crossover recombination. However, gene-conversion is an important, and more common, form of (two-crossover) recombination which has been much less investigated in the algorithms literature. 
 
In this paper we explicitly incorporate gene-conversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossing-over and gene-conversion (along with single-nucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of gene-conversion into recently developed discrete methods [20, 26] that compute lower and upper-bound information on the amount of needed recombination without gene-conversion. We first examine the most natural extension of the lower bound methods from [20], showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integer-linear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed single-crossovers and gene-conversions, along with explicit networks showing a putative history of mutations, single-crossovers and gene-conversions. 
 
We validate the significance of these methods by showing that they can be effectively used to distinguish simulation-derived sequences generated without gene-conversion from sequences that were generated with gene-conversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified [22], where gene-conversion may have played a significant role. Demonstration software is available at www.cs. ucdavis.edu/~gusfield.
14072276
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees
We present an efficient algorithm for statistical multiple alignment based on the TKF91 model of Thorne, Kishino, and Felsenstein (1991) on an arbitrary k-leaved phylogenetic tree. The existing algorithms use a hidden Markov model approach, which requires at least O( radical 5(k)) states and leads to a time complexity of O(5(k)L(k)), where L is the geometric mean sequence length. Using a combinatorial technique reminiscent of inclusion/exclusion, we are able to sum away the states, thus improving the time complexity to O(2(k)L(k)) and considerably reducing memory requirements. This makes statistical multiple alignment under the TKF91 model a definite practical possibility in the case of a phylogenetic tree with a modest number of leaves.
23745644
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks
Under the infinite-sites model of mutation, we consider the problem of finding the minimum number of recombination events which must have occurred in the evolutionary history of sampled DNA sequences. Our approach is deterministic and is based on the combinatorics of leaf-labelled rooted trees. In contrast to previously known approaches, which only yield estimated lower bounds, our approach always gives the exact minimum number of recombination events. Furthermore, our method can be used to reconstruct explicitly evolutionary histories with the minimum number of recombination events. As an additional application, we discuss how our work can be used to define haplotype blocks.
7144496
Loss-tolerant QoS using firm constraints in guaranteed rate networks
We propose a trade-off between hard and soft real-time guarantees to maintain an acceptable QoS guarantee in overload condition and maximize efficiently the utilization of network resources. The key of our solution is that many real-time applications are loss-tolerant, but the loss profile must be well defined since successive packet losses are not suitable. We use the concept of (m,k)-firm timing constraints to define a novel guaranteed loss-tolerant QoS. Therefore, we extend the basic WFQ algorithm to take into account the firm timing constraints to provide lower delay guarantees without violating bandwidth fairness or misusing network resources. The proposal is called (m,k)-WFQ. Using network calculus formalism, analytic study gives the deterministic delay bound provided by the (m,k)-WFQ algorithm for upper bounded arrival curve traffic. Theoretical results and simulations show a noticeable improvement on delay guarantee made by (m,k)-WFQ compared to standard WFQ algorithm without much degrading bandwidth fairness.
564335
Automatic organization for digital photographs with geographic coordinates
6362823
Assigning textual names to sets of geographic coordinates
NameSet is a system that translates a set of geographic coordinates into a textual name based on the geographic regions where the coordinates occur. One possible application of NameSet is to concisely present the geographical scope of a set of geo-referenced observations to a human user. Another application is to generate text to depict a set of coordinates that appear on a web site -- text that could later be used for information retrieval applications. NameSet's computation is based on a simple algorithm, using off-the-shelf and web-based data sources. The system was proven effective in an application that automatically organizes and names sets of geo-referenced digital photographs.
9240638
An Irregular Search Window Reuse Scheme for Motion Estimation in MPEG-2 to H.264 Transcoding
Motion estimation (ME) is a computation-intensive operation in video coding system. In MPEG-2 to H.264 transcoding, motion vector (MV) from MPEG-2 reused as search center in H.264 encoder is a simple but effective technique to simplify ME procedure. However directly introducing MPEG-2 MV will bring irregular overlapping between search windows of successive macroblocks (MB) which invalidates the data reuse scheme in hardware design of ME module. In this paper, the authors propose a search window reuse scheme for transcoding in HDTV application. By utilizing the similarity between neighboring MVs, overlapping of search windows between successive MBs can be regularized. Experiment results show that our method achieve average 93.1% search window reuse rate in HDTV sequence with almost no video quality degradation. And the bandwidth can be reduced to 92.5 Mbytes/s based on theoretical calculation which is only 40.6% of that without this scheme.
2185149
Monocular perception of biological motion-detection and labeling
Computer perception of biological motion is key to developing convenient and powerful human-computer interfaces. Successful body tracking algorithms have been developed; however initialization is done by hand. We propose a method for detecting a moving human body and for labeling its parts automatically. It is based on maximizing the joint probability density function (PDF) of the position and velocity of the body parts. The PDF is estimated from training data. Dynamic programming is used for calculating efficiently the best global labeling on an approximation of the PDF. The computational cost is on the order of N/sup 4/ where N is the number of features detected. We explore the performance of our method with experiments carried on a variety of periodic and non-periodic body motions viewed monocularly for a total of approximately 30,000 frames. Point-markers were strapped to the joints of the subject for facilitating image analysis. We find an average of 2.3% labeling error; the experiments also suggest a high degree of viewpoint-invariance.