Probability Of Alignment Research Articles

Statistical Significance of Optical Map Alignments

The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities.

Impacted upper canines: examination and treatment proposal based on 3D versus 2D diagnosis

The purpose of this diagnostic cross-over study was to evaluate whether three-dimensional (3D) diagnostics (cone-beam computed tomography, CBCT) was superior to two-dimensional (2D) diagnostics (panoramic X-ray, OPG) in patients with impacted upper canines for assessing their position and the probability of their alignment. Panoramic X-rays, CBCTs, and study casts of 21 patients with a total of 29 impacted maxillary canines were analyzed. Patients with syndromes or tooth aplasias were excluded. A total of 26 dentists of various specialist disciplines rated different parameters, such as canine position and their probability of alignment as well as their relation to and resorption of adjacent teeth. 2D X-rays and study casts were rated first; then 3D images and casts were evaluated at least 2 weeks later. The actual level of displacement was defined by two trained examiners and labeled as the master finding, according to modified criteria established by Ericson and Kurol (1988). In 64% of all patients, canine position was assessed concordantly in 2D and 3D images. 2D assessments were in slight agreement (κ = 0.374), while 3D ratings were in good agreement with the master findings (κ = 0.714). Two-thirds of the canines' apical regions were judged identifiable in 2D and 3D images; more than 1/4 of the canines' apices were not identifiable in 2D images, but were identifiable in 3D images. The diagnosis of lateral incisor root resorption in the CBCT agreed well with the master finding (κ = 0.634), but examiners overlooked slight resorption in 20% of the patients. In 82% of the patients teeth, treatment suggestions (orthodontic alignment or surgical removal) were the same for 2D and 3D images. Canine inclination visible in the panoramic X-rays was the most important factor influencing the treatment proposal. Small volume CBCT may be justified as a supplement to a routine panoramic X-ray in the following cases: when canine inclination in the panoramic X-ray exceeds 30°, when root resorption of adjacent teeth is suspected, and/or when the canine apex is not clearly discernible in the panoramic X-ray, implying dilaceration of the canine root. We intend to validate the results of this study in a clinical trial.

Helical Properties of Sheared and Rotating Turbulence

Helical properties of two homogeneous turbulent flows are compared by using velocity fields obtained by means of direct numerical simulation (DNS). Probability distribution functions (PDFs) of relative helicity show a preference for two-dimensionalization in the case of growing shear-driven turbulence, while an approximately equidistribution is obtained for the case of rotating turbulence. PDFs of super-helicity show a higher probability for alignment or anti-alignment of vorticity with dissipation of velocity in both cases. Isovorticity surfaces colored with relative helicity and relative super-helicity show that the signs of the two quantities tend to be strongly correlated again in both cases. This sign correlation is further quantified by their joint PDF and it suggests that super-helicity dissipates helicity.

AREM: aligning short reads from ChIP-sequencing by expectation maximization.

High-throughput sequencing coupled to chromatin immunoprecipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin modifiers, and other DNA binding proteins. A key step in ChIP-Seq data analysis is to map short reads from high-throughput sequencing to a reference genome and identify peak regions enriched with short reads. Although several methods have been proposed for ChIP-Seq analysis, most existing methods only consider reads that can be uniquely placed in the reference genome, and therefore have low power for detecting peaks located within repeat sequences. Here, we introduce a probabilistic approach for ChIP-Seq data analysis that utilizes all reads, providing a truly genome-wide view of binding patterns. Reads are modeled using a mixture model corresponding to K enriched regions and a null genomic background. We use maximum likelihood to estimate the locations of the enriched regions, and implement an expectation-maximization (E-M) algorithm, called AREM (aligning reads by expectation maximization), to update the alignment probabilities of each read to different genomic locations. We apply the algorithm to identify genome-wide binding events of two proteins: Rad21, a component of cohesin and a key factor involved in chromatid cohesion, and Srebp-1, a transcription factor important for lipid/cholesterol homeostasis. Using AREM, we were able to identify 19,935 Rad21 peaks and 1,748 Srebp-1 peaks in the mouse genome with high confidence, including 1,517 (7.6%) Rad21 peaks and 227 (13%) Srebp-1 peaks that were missed using only uniquely mapped reads. The open source implementation of our algorithm is available at http://sourceforge.net/projects/arem.

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses. In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.

Computing an optimal time window of audiovisual integration in focused attention tasks: illustrated by studies on effect of age and prior knowledge

The concept of a "time window of integration" holds that information from different sensory modalities must not be perceived too far apart in time in order to be integrated into a multisensory perceptual event. Empirical estimates of window width differ widely, however, ranging from 40 to 600ms depending on context and experimental paradigm. Searching for theoretical derivation of window width, Colonius and Diederich (Front Integr Neurosci 2010) developed a decision-theoretic framework using a decision rule that is based on the prior probability of a common source, the likelihood of temporal disparities between the unimodal signals, and the payoff for making right or wrong decisions. Here, this framework is extended to the focused attention task where subjects are asked to respond to signals from a target modality only. Evoking the framework of the time-window-of-integration (TWIN) model, an explicit expression for optimal window width is obtained. The approach is probed on two published focused attention studies. The first is a saccadic reaction time study assessing the efficiency with which multisensory integration varies as a function of aging. Although the window widths for young and older adults differ by nearly 200ms, presumably due to their different peripheral processing speeds, neither of them deviates significantly from the optimal values. In the second study, head saccadic reactions times to a perfectly aligned audiovisual stimulus pair had been shown to depend on the prior probability of spatial alignment. Intriguingly, they reflected the magnitude of the time-window widths predicted by our decision-theoretic framework, i.e., a larger time window is associated with a higher prior probability.

FEAST: Sensitive Local Alignment with Multiple Rates of Evolution

We present a pairwise local aligner, FEAST, which uses two new techniques: a sensitive extension algorithm for identifying homologous subsequences, and a descriptive probabilistic alignment model. We also present a new procedure for training alignment parameters and apply it to the human and mouse genomes, producing a better parameter set for these sequences. Our extension algorithm identifies homologous subsequences by considering all evolutionary histories. It has higher maximum sensitivity than Viterbi extensions, and better balances specificity. We model alignments with several submodels, each with unique statistical properties, describing strongly similar and weakly similar regions of homologous DNA. Training parameters using two submodels produces superior alignments, even when we align with only the parameters from the weaker submodel. Our extension algorithm combined with our new parameter set achieves sensitivity 0.59 on synthetic tests. In contrast, LASTZ with default settings achieves sensitivity 0.35 with the same false positive rate. Using the weak submodel as parameters for LASTZ increases its sensitivity to 0.59 with high error. FEAST is available at http://monod.uwaterloo.ca/feast/.

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences

In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA sequences. Both PicXAA and PicXAA-R are probabilistic non-progressive alignment algorithms that aim to find the optimal alignment of multiple biological sequences by maximizing the expected accuracy. PicXAA and PicXAA-R greedily build up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures local similarities among sequences. PicXAA-Web integrates these two algorithms in a user-friendly web platform for accurate alignment and analysis of multiple protein, DNA and RNA sequences. PicXAA-Web can be freely accessed at http://gsp.tamu.edu/picxaa/.

THE WIDEST-SEPARATION SUBSTELLAR COMPANION CANDIDATE TO A BINARY T TAURI STAR

The results of near-infrared imaging and spectroscopy of a substellar companion (SR12?C), with a possible planetary mass, of a binary T Tauri star (SR12?AB) in the ? Ophiuchi star-forming region are presented. The object is separated by ~87, corresponding to ~1100?AU at 125?pc, and has an H-band brightness of 15.2 mag and infrared spectra suggesting a spectral type of M9.0 ? 0.5. It is confirmed that SR12?C is physically related to the ? Ophiuchi star-forming region from its common proper motion with SR12?AB and its youth is confirmed by a gravity-sensitive spectral feature. Furthermore, based on the number of known members of the ? Ophiuchi star-forming region in the area in which SR12?AB exists, the probability of a chance alignment is ~1% and it is therefore likely that SR12?C is physically associated with SR12?AB. The mass of SR12?C is estimated by comparing its estimated luminosity and assumed age with the theoretical age-luminosity relation. SR12?C is identified as an extremely low-mass (0.013?? 0.007 M ?) object, but its separation from its parent star is the widest among planetary-mass companion (PMC) candidates imaged to date. In addition, SR12?C is the first PMC candidate directly imaged around a binary star. This discovery suggests that PMCs form via multiple star formation processes including disk gravitational instability and cloud core fragmentation.

Multiple Linear Regression for Extracting Phrase Translation Pairs

Phrase translation pairs are very useful for bilingual lexicography, machine translation system, cross-lingual information retrieval and many applications in natural language processing. Phrase translation pairs are always extracted from bilingual sentence pairs. In this paper, we extract phrase translation pairs based on word alignment results of Chinese-English bilingual sentence pairs and parsing trees of Chinese sentences, in order to decrease the influence of the grammar disagreement between Chinese and English. Discriminative features for phrase translation pairs are proposed to evaluate extracted ones in this paper, including translation literality, phrase alignment probability and phrase length difference. Multiple linear regression model combined with N-best strategy will be employed to filter phrase translation pairs, in order to improve the evaluating and filtering performance. Experimental results indicate that the filtering performance of phrase alignment probability is best in three kinds of discriminative features for evaluating Chinese-English phrase translation pairs. After multiple linear regression model combined with N-best strategy is used, its F1 achieves 86.24%.

PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach

BackgroundAccurate and efficient structural alignment of non-coding RNAs (ncRNAs) has grasped more and more attentions as recent studies unveiled the significance of ncRNAs in living organisms. While the Sankoff style structural alignment algorithms cannot efficiently serve for multiple sequences, mostly progressive schemes are used to reduce the complexity. However, this idea tends to propagate the early stage errors throughout the entire process, thereby degrading the quality of the final alignment. For multiple protein sequence alignment, we have recently proposed PicXAA which constructs an accurate alignment in a non-progressive fashion.ResultsHere, we propose PicXAA-R as an extension to PicXAA for greedy structural alignment of ncRNAs. PicXAA-R efficiently grasps both folding information within each sequence and local similarities between sequences. It uses a set of probabilistic consistency transformations to improve the posterior base-pairing and base alignment probabilities using the information of all sequences in the alignment. Using a graph-based scheme, we greedily build up the structural alignment from sequence regions with high base-pairing and base alignment probabilities.ConclusionsSeveral experiments on datasets with different characteristics confirm that PicXAA-R is one of the fastest algorithms for structural alignment of multiple RNAs and it consistently yields accurate alignment results, especially for datasets with locally similar sequences. PicXAA-R source code is freely available at: http://www.ece.tamu.edu/~bjyoon/picxaa/.

Strain-Release Assembly of Nanowires on Stretchable Substrates

A simple yet effective method for assembly of highly aligned nanowires (NWs) on stretchable substrates is reported. In this method, NWs were first transferred to a strained stretchable substrate. After the strain was released, the NWs aligned in the transverse direction and the area coverage of the NWs on the substrate increased. This method can be applied to any NWs deposited on a stretchable film and can be repeated multiple times to increase the alignment and density of the NWs. For silver (Ag) and silicon (Si) NWs on poly(dimethylsiloxane) (PDMS) substrates, the probability of NW alignment increased from 29% to 90% for Ag NWs, and from 25% to 88% for Si NWs after two assembly steps; the density increased by 60% and 75% for the Ag and Si NWs, respectively. The large-strain elasticity of the substrate and the static friction between the NWs and the substrate play key roles in this assembly method. We find that a model that takes into account the volume incompressibility of PDMS reliably predicts the degree of NW alignment and NW density. The utility of this assembly method was demonstrated by fabricating a strain sensor array composed of aligned Si NWs on a PDMS substrate, with a device yield of 95%.

A WIDELY SEPARATED, HIGHLY OCCLUDED COMPANION TO THE NEARBY LOW-MASS T TAURI STAR TWA 30

We report the discovery of TWA 30B, a wide (~3400 AU), co-moving M dwarf companion to the nearby (~42 pc) young star TWA 30. Companionship is confirmed from their statistically consistent proper motions and radial velocities, as well as a chance alignment probability of only 0.08%. Like TWA 30A, the spectrum of TWA 30B shows signatures of an actively accreting disk (H I and alkali line emission) and forbidden emission lines tracing outflowing material ([O I], [O II], [O III], [S II], and [N II]). We have also detected [C I] emission in the optical data, marking the first such detection of this line in a pre-main sequence star. Negligible radial velocity shifts in the emission lines relative to the stellar frame of rest (Delta V < 30 km/s) indicate that the outflows are viewed in the plane of the sky and that the corresponding circumstellar disk is viewed edge-on. Indeed, TWA 30B appears to be heavily obscured by its disk, given that it is 5 magnitudes fainter than TWA 30A at K-band despite having a slightly earlier spectral type (M4 versus M5). The near-infrared spectrum of TWA 30B also evinces an excess that varies on day timescales, with colors that follow classical T Tauri tracks as opposed to variable reddening (as is the case for TWA 30A). Multi-epoch data show this excess to be well-modeled by a blackbody component with temperatures ranging from 630 to 880 K and emitting areas that scale inversely with the temperature. The variable excess may arise from disk structure such as a rim or a warp at the inner disk edge located at a radial distance of ~3-5 R_sun. As the second and third closest actively accreting and outflowing stars to the Sun (after TWA 3), TWA 30AB presents an ideal system for detailed study of star and planetary formation processes at the low-mass end of the hydrogen-burning spectrum.

How does informativeness affect prosodic prominence?

A key function of prosodic prominence is to mark the most informative words in an utterance. However, informativeness has been conceptualised as, e.g., focus, given/new status or predictability; it is not clear how these are related. Furthermore, prominence is constrained by metrical prosodic structure. We present a new framework for prominence production: informativeness and prosodic factors are constraints on the probabilistic alignment of words with metrical structure. Informativeness operates on two levels, focus and lexical “accentability” (predictability, part-of-speech). Foci align with nuclear accents, however, this is affected by prosodic and “accentability” constraints. Accent prediction models (nuclear, non-nuclear, or unaccented) are presented for the Switchboard corpus. Consistent with our predictions, nuclear accents are more likely later in a phrase, and on focused words. The likelihood of nuclear and non-nuclear accents is affected by prosodic constraints (e.g., rhythm) and “accentability”. The implications for the role of prosody in language production are discussed.

Discovery of the afterglow and host galaxy of the low-redshift short GRB 080905A★

We present the discovery of short GRB 080905A, its optical afterglow and host galaxy. Initially discovered by Swift, our deep optical observations enabled the identification of a faint optical afterglow, and subsequently a face-on spiral host galaxy underlying the GRB position, with a chance alignment probability of <1%. There is no supernova component present in the afterglow to deep limits. Spectroscopy of the galaxy provides a redshift of z=0.1218, the lowest redshift yet observed for a short GRB. The GRB lies offset from the host galaxy centre by ~18.5 kpc, in the northern spiral arm which exhibits an older stellar population than the southern arm. No emission lines are visible directly under the burst position, implying little ongoing star formation at the burst location. These properties would naturally be explained were the progenitor of GRB 080905A a compact binary merger.

THEORY OF INCOMPRESSIBLE MAGNETOHYDRODYNAMIC TURBULENCE WITH SCALE-DEPENDENT ALIGNMENT AND CROSS-HELICITY

(Abridged) An anisotropic theory of MHD turbulence with nonvanishing cross-helicity is constructed based on Boldyrev's alignment hypothesis and probabilities p and q for fluctuations v and b to be positively or negatively aligned. Guided by observations suggesting that the normalized cross-helicity and the probability p are approximately constant in the inertial range, a generalization of Boldyrev's theory is derived that depends on the three ratios w+/w-, epsilon+/epsilon-, and p/q. The theory reduces to Boldyrev's original theory when w+ = w-, epsilon+ = epsilon-, and p = q.

ProgressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

BackgroundMultiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms.Methodology/Principal FindingsWe describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The new genome alignment algorithm demonstrates high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental gain and loss. We apply the new algorithm to a set of 23 genomes from the genera Escherichia, Shigella, and Salmonella. Analysis of whole-genome multiple alignments allows us to extend the previously defined concepts of core- and pan-genomes to include not only annotated genes, but also non-coding regions with potential regulatory roles. The 23 enterobacteria have an estimated core-genome of 2.46Mbp conserved among all taxa and a pan-genome of 15.2Mbp. We document substantial population-level variability among these organisms driven by segmental gain and loss. Interestingly, much variability lies in intergenic regions, suggesting that the Enterobacteriacae may exhibit regulatory divergence.ConclusionsThe multiple genome alignments generated by our software provide a platform for comparative genomic and population genomic studies. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve.

SLOAN LOW-MASS WIDE PAIRS OF KINEMATICALLY EQUIVALENT STARS (SLoWPoKES): A CATALOG OF VERY WIDE, LOW-MASS PAIRS

We present the Sloan Low-mass Wide Pairs of Kinematically Equivalent Stars (SLoWPoKES), a catalog of 1342 very-wide (projected separation >500 AU), low-mass (at least one mid-K--mid-M dwarf component) common proper motion pairs identified from astrometry, photometry, and proper motions in the Sloan Digital Sky Survey. A Monte Carlo based Galactic model is constructed to assess the probability of chance alignment for each pair; only pairs with a probability of chance alignment </= 0.05 are included in the catalog. The overall fidelity of the catalog is expected to be 98.35%. The selection algorithm is purposely exclusive to ensure that the resulting catalog is efficient for follow-up studies of low-mass pairs. The SLoWPoKES catalog is the largest sample of wide, low-mass pairs to date and is intended as an ongoing community resource for detailed study of bona fide systems. Here we summarize the general characteristics of the SLoWPoKES sample and present preliminary results describing the properties of wide, low-mass pairs. While the majority of the identified pairs are disk dwarfs, there are 70 halo subdwarf pairs and 21 white dwarf-disk dwarf pairs, as well as four triples. Most SLoWPoKES pairs violate the previously defined empirical limits for maximum angular separation or binding energies. However, they are well within the theoretical limits and should prove very useful in putting firm constraints on the maximum size of binary systems and on different formation scenarios. We find a lower limit to the wide binary frequency for the mid-K-mid-M spectral types that constitute our sample to be 1.1%. This frequency decreases as a function of Galactic height, indicating a time evolution of the wide binary frequency. [See text for full abstract.]

Limits on radioactive powered emission associated with a short-hard GRB 070724A in a star-forming galaxy

We present results of an extensive observing campaign of the short duration, hard spectrum gamma-ray burst (GRB) 070724A, aimed at detecting the radioactively-powered emission that might follow from a binary merger or collapse involving compact objects. Our multi-band observations span the range in time over which this so-called Li-Paczynski mini-supernova could be active, beginning within 3 hours of the GRB trigger, and represent some of the deepest and most comprehensive searches for such emission. We find no evidence for such activity and place limits on the abundances and the lifetimes of the possible radioactive nuclides that could form in the rapid decompression of nuclear-density matter. Furthermore, our limits are significantly fainter than the peak magnitude of any previously detected broad-lined Type Ic supernova (SN) associated with other GRBs, effectively ruling out a long GRB-like SN for with this event. Given the unambiguous redshift of the host galaxy (z=0.456), GRB 070724A represents one of a small, but growing, number of short-hard GRBs for which firm physical/restframe quantities currently exist. The host of GRB 070724A is a moderately star-forming galaxy with an older stellar population component and a relatively high metallicity of 12+log(O/H)_KD02=9.1. We find no significant evidence for large amounts of extinction along the line of sight that could mask the presence of a SN explosion and estimate a small probability for chance alignment with the putative host. We discuss how our derived constraints fit into the evolving picture of short-hard GRBs, their potential progenitors, and the host environments in which they are thought to be produced.

Acquired prior knowledge modulates audiovisual integration

Orienting responses to audiovisual events in the environment can benefit markedly by the integration of visual and auditory spatial information. However, logically, audiovisual integration would only be considered successful for stimuli that are spatially and temporally aligned, as these would be emitted by a single object in space-time. As humans do not have prior knowledge about whether novel auditory and visual events do indeed emanate from the same object, such information needs to be extracted from a variety of sources. For example, expectation about alignment or misalignment could modulate the strength of multisensory integration. If evidence from previous trials would repeatedly favour aligned audiovisual inputs, the internal state might also assume alignment for the next trial, and hence react to a new audiovisual event as if it were aligned. To test for such a strategy, subjects oriented a head-fixed pointer as fast as possible to a visual flash that was consistently paired, though not always spatially aligned, with a co-occurring broadband sound. We varied the probability of audiovisual alignment between experiments. Reaction times were consistently lower in blocks containing only aligned audiovisual stimuli than in blocks also containing pseudorandomly presented spatially disparate stimuli. Results demonstrate dynamic updating of the subject's prior expectation of audiovisual congruency. We discuss a model of prior probability estimation to explain the results.