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A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

ABSTRACT: The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa, revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka.

SUBMITTER: Romero JR

PROVIDER: S-EPMC5089818 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

Romero José R JR Carballido Jessica A JA Garbus Ingrid I Echenique Viviana C VC Ponzoni Ignacio I

Evolutionary bioinformatics online 20161030

The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, ...[more]

PMID: 27812277

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Project description:BackgroundMore so than face-to-face counseling, users of online text-based services might drop out from a session before establishing a clear closure or expressing the intention to leave. Such premature departure may be indicative of heightened risk or dissatisfaction with the service or counselor. However, there is no systematic way to identify this understudied phenomenon.PurposeThis study has two objectives. First, we developed a set of rules and used logic-based pattern matching techniques to systematically identify premature departures in an online text-based counseling service. Second, we validated the importance of premature departure by examining its association with user satisfaction. We hypothesized that the users who rated the session as less helpful were more likely to have departed prematurely.MethodWe developed and tested a classification model using a sample of 575 human-annotated sessions from an online text-based counseling platform. We used 80% of the dataset to train and develop the model and 20% of the dataset to evaluate the model performance. We further applied the model to the full dataset (34,821 sessions). We compared user satisfaction between premature departure and completed sessions based on data from a post-session survey.ResultsThe resulting model achieved 97% and 92% F1 score in detecting premature departure cases in the training and test sets, respectively, suggesting it is highly consistent with the judgment of human coders. When applied to the full dataset, the model classified 15,150 (43.5%) sessions as premature departure and the remaining 19,671 (56.5%) as completed sessions. Completed cases (15.2%) were more likely to fill the post-chat survey than premature departure cases (4.0%). Premature departure was significantly associated with lower perceived helpfulness and effectiveness in distress reduction.ConclusionsThe model is the first that systematically and accurately identifies premature departure in online text-based counseling. It can be readily modified and transferred to other contexts for the purpose of risk mitigation and service evaluation and improvement.

Project description:A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using model data and templates calculated at a resolution of 2.6 A. Owing to this independence of errors, information from the new map can be combined in a simple fashion with information from the original map to create an improved map. An iterative phase-improvement process using this approach and other applications of the image-reconstruction method are described and applied to experimental data at resolutions ranging from 2.4 to 2.8 A.

Dataset Information

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

Publications

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

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