Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results

Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs. Unfortunately, the annotation of ncRNA genes that give rise to functional RNA molecules has begun only recently, and it is far from being complete. Considering the huge amount of genome sequence data, we need efficient computational methods for finding ncRNA genes. One effective way of finding ncRNA genes is to look for regions that are similar to known ncRNA genes. As many ncRNAs have well-conserved secondary structures, we need statistical models that can represent such structures for this purpose. In this paper, we propose a new method for representing RNA sequence profiles and finding structural alignment of RNAs based on profile context-sensitive hidden Markov models (profile-csHMMs). Unlike existing models, the proposed approach can handle any kind of RNA secondary structures, including pseudoknots. We show that profile-csHMMs can provide an effective framework for the computational analysis of RNAs and the identification of ncRNA genes

Performance Following: Real-Time Prediction of Musical Sequences Without a Score

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Robust Mobile Object Tracking Based on Multiple Feature Similarity and Trajectory Filtering

This paper presents a new algorithm to track mobile objects in different scene conditions. The main idea of the proposed tracker includes estimation, multi-features similarity measures and trajectory filtering. A feature set (distance, area, shape ratio, color histogram) is defined for each tracked object to search for the best matching object. Its best matching object and its state estimated by the Kalman filter are combined to update position and size of the tracked object. However, the mobile object trajectories are usually fragmented because of occlusions and misdetections. Therefore, we also propose a trajectory filtering, named global tracker, aims at removing the noisy trajectories and fusing the fragmented trajectories belonging to a same mobile object. The method has been tested with five videos of different scene conditions. Three of them are provided by the ETISEO benchmarking project (http://www-sop.inria.fr/orion/ETISEO) in which the proposed tracker performance has been compared with other seven tracking algorithms. The advantages of our approach over the existing state of the art ones are: (i) no prior knowledge information is required (e.g. no calibration and no contextual models are needed), (ii) the tracker is more reliable by combining multiple feature similarities, (iii) the tracker can perform in different scene conditions: single/several mobile objects, weak/strong illumination, indoor/outdoor scenes, (iv) a trajectory filtering is defined and applied to improve the tracker performance, (v) the tracker performance outperforms many algorithms of the state of the art