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Long noncoding RNAs (lncRNAs) which were initially dismissed as "transcriptional noise" have become a vital area of study after their roles in biological regulation were discovered. Long noncoding RNAs have been implicated in various developmental processes and diseases. Here, we perform exon mapping of human lncRNA sequences (taken from National Center for Biotechnology Information GenBank) using digital filters. Antinotch digital filters are used to map out the exons of the lncRNA sequences analyzed. The period 3 property which is an established indicator for locating exons in genes is used here. Discrete wavelet transform filter bank is used to fine-tune the exon plots by selectively removing the spectral noise. The exon locations conform to the ranges specified in GenBank. In addition to exon prediction, G-C concentrations of lncRNA sequences are found, and the sequences are searched for START and STOP codons as these are indicators of coding potential. [ABSTRACT FROM AUTHOR]

Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers. [ABSTRACT FROM AUTHOR]

The performance of image processing algorithms can be significantly improved by the application of multi‐resolution image representation with directional features. Directionlet transform (DT) is one such representation which has gained popularity over the past few years as an anisotropic, perfect reconstruction and critically sampled basis function with directional vanishing moments along any two directions. In this study, the authors propose a spatially adaptive image denoising scheme for Gaussian noise based on DT by considering the dependences of the directionlet coefficients across different scales. The image is first decomposed using DT and the coefficients so obtained are modelled using a bivariate heavy tailed 'pdf' with a local variance parameter to account for inter‐ and intra‐scale dependencies of the coefficients. The DT is made adaptive to the local dominant directions in the image by identifying the dominant directions in the spatially segmented image through the computation of a parameter called 'directional variance'. Bayesian 'maximum a posteriori' estimator is then used to compute the noise free coefficients from the bivariate models of the signal and noise. The denoised image is obtained from the transform coefficients, which were modified using the bivariate shrinkage function, using directional information and inverse DT. Experimental results show that the bivariate shrinkage in directionlet domain achieves better performance than that in wavelet domain, in terms of numerical and perceptual quality. [ABSTRACT FROM AUTHOR]

Background: This paper compares the most common digital signal processing methods of exon prediction in eukaryotes, and also proposes a technique for noise suppression in exon prediction. The specimen used here which has relevance in medical research, has been taken from the public genomic database - GenBank. Methods: Here exon prediction has been done using the digital signal processing methods viz. binary method, EIIP (electron-ion interaction psuedopotential) method and filter methods. Under filter method two filter designs, and two approaches using these two designs have been tried. The discrete wavelet transform has been used for de-noising of the exon plots. Results: Results of exon prediction based on the methods mentioned above, which give values closest to the ones found in the NCBI database are given here. The exon plot de-noised using discrete wavelet transform is also given. Conclusion: Alterations to the proven methods as done by the authors, improves performance of exon prediction algorithms. Also it has been proven that the discrete wavelet transform is an effective tool for de-noising which can be used with exon prediction algorithms. [ABSTRACT FROM AUTHOR]

The database search method is a widely accepted method to assign a peptide to the tandem mass spectra. In this study, a new flexible method- FPTMS is introduced to interpret the tandem mass spectra with the known peptide sequences in a protein database. Here the frequency of occurrence of fragment ion peaks extracted from the extensive spectral library is used to predict the theoretical tandem mass spectra of the peptides. The dot product scoring and windowed-xcorr scoring methods were implemented to score the experimental spectrum against the theoretical peptide spectra. Windowed-xcorr is introduced to tackle the mass errors and the cleavage position of the fragmentation process. The new method with windowed-xcorr shows an improved identification rate compared to the existing search engines Crux-Tide and X!Tandem at 1% False Discovery Rate (FDR) for the dataset considered in this study. Identifying or sequencing of the peptide from tandem mass spectra is an important application in mass spectrometry-based proteomics. Collision-induced dissociation (CID) fragmentation spectra have been widely used to develop a peptide identification algorithm using database search strategy. CID fragmentation behavior is a complex process and found to have dependency on the sequences of peptide, charge state, and residue content. The inclusion of more features of peptide fragmentation behavior and adaptable scoring algorithm improves the efficiency of the peptide identification algorithm. Unlabelled Image • FPTMS identifies the peptide from the low energy CID spectrum of tryptic peptides. • The relative frequency of occurrence of fragment ion feature is used to predict the theoretical spectrum of the peptide reliably. • Sliding window cross-correlation is used for scoring the experimental spectrum against the candidate peptide spectrum. • FPTMS(windowed-xcorr) shows an improved identification rate compared to existing algorithms: Crux-Tide & X!Tandem at 1% FDR. [ABSTRACT FROM AUTHOR]

Document forgeries that involve modification of the materials used, such as ink and paper, provide evidence of any malpractices being performed. Forensic specialists use different techniques to identify and classify these samples; however, the most preferred method is to use nondestructive techniques to avoid any potential damage to the original specimen under investigation. Hyperspectral imaging has already been explored in several application domains and used as a powerful method in forensic investigations to extract information about the materials under examination. To precisely classify the material information and utilize the hyperspectral imaging technique's potential, we probed the potential of some hybrid spectral similarity measures to classify different commonly used paper samples. A comparison of these methods is quantitatively presented in this article. Hybrid spectral similarity algorithms are tested on forensic analysis of paper data. We compared the classification capabilities of various hybrid spectral similarity algorithms on hyperspectral data of 40 different paper samples. The overall accuracy (OA), kappa K̂, Z‐score of kappa (ZK̂), and the 95% confidence interval of kappa (CI(K̂)) are used for comparison. The SID‐SAM and SID‐SCA produced an overall accuracy of 88% and 87%, respectively, which is highest among the hybrid spectral similarity measures tested. [ABSTRACT FROM AUTHOR]