This article presents a linear motor mover position detection method based on an image sample database to achieve high-precision measurement of the position of a long-stroke linear motor mover. First, the aperiodic fringe image is constructed with a chirp signal as the target shooting source, and an image sample database is established by capturing the target image with a certain acquisition frequency using a line-scan camera. Second, a normalized correlation coefficient (NCC) matching method is proposed to search for the position of the current image in the database. A coarse positioning method based on velocity estimation is also employed to improve the efficiency of position matching in the sample database. Third, to overcome the position measurement error caused by incomplete matching between the current image and the image in the database, a subpixel measurement algorithm based on local upsampling NCC is proposed to improve the measurement accuracy. Finally, the actual displacement of the actuator is obtained by combining the calibration coefficients. To verify the feasibility of the proposed method, an experimental platform is built using a line-scan camera, a linear motor, an adjustable light source, and a target source image. Comparison tests, speed adaptation experiments, and light adaptation experiments are set up. The experimental results show that the average time of the proposed method is approximately 1 ms, and the average absolute measurement error is approximately 0.005 mm under various working conditions, which shows that the proposed method has real-time performance and strong environmental adaptability.

The WebSTAR3D web server is a user-friendly online interface for the alignment of RNA 3D structures. The website takes as input two files, each of which can be in either PDB or mmCIF format, containing the desired structures to align, via a PDB code or user upload. In return, the user is presented with a visualization of the aligned structures in Jmol or JSmol, along with the corresponding sequence alignment, and the option to download the nucleotide mapping of the structures and a PDB file containing the aligned, superimposed structures. AVAILABILITY AND IMPLEMENTATION: The WebSTAR3D is available at http://rna.ucf.edu/WebSTAR3D CONTACT: [email protected].

BACKGROUND: Recent advances in RNA structure probing technologies, including the ones based on high-throughput sequencing, have improved the accuracy of thermodynamic folding with quantitative nucleotide-resolution structural information. RESULTS: In this paper, we present a novel approach, ProbeAlign, to incorporate the reactivities from high-throughput RNA structure probing into ncRNA homology search for functional annotation. To reduce the overhead of structure alignment on large-scale data, the specific pairing patterns in the query sequences are ignored. On the other hand, the partial structural information of the target sequences embedded in probing data is retrieved to guide the alignment. Thus the structure alignment problem is transformed into a sequence alignment problem with additional reactivity information. The benchmark results show that the prediction accuracy of ProbeAlign outperforms filter-based CMsearch with high computational efficiency. The application of ProbeAlign to the FragSeq data, which is based on genome-wide structure probing, has demonstrated its capability to search ncRNAs in a large-scale dataset from high-throughput sequencing. CONCLUSIONS: By incorporating high-throughput sequencing-based structure probing information, ProbeAlign can improve the accuracy and efficiency of ncRNA homology search. It is a promising tool for ncRNA functional annotation on genome-wide datasets. AVAILABILITY: The source code of ProbeAlign is available at http://genome.ucf.edu/ProbeAlign.

BACKGROUND: RNAalifold, a popular computational method for RNA consensus structure prediction, incorporates covarying mutations into a thermodynamic model to fold the aligned RNA sequences. When quantifying covariance, it evaluates conserved signals of two aligned columns with base-pairing rules. This scoring scheme performs better than some other approaches, such as mutual information. However it ignores the phylogenetic history of the aligned sequences, which is an important criterion to evaluate the level of sequence covariance. RESULTS: In this article, in order to improve the accuracy of consensus structure folding, we propose a novel approach named PhyloRNAalifold. It incorporates the number of covarying mutations on the phylogenetic tree of the aligned sequences into the covariance scoring of RNAalifold. The benchmarking results show that the new scoring scheme of PhyloRNAalifold can improve the consensus structure detection of RNAalifold. CONCLUSION: Incorporating additional phylogenetic information of aligned sequences into the covariance scoring of RNAalifold can improve its performance of consensus structures folding. This improvement is correlated with alignment characteristics, such as pair-wise identity and the number of sequences in the alignment.