Dataset Information

Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform.

ABSTRACT: BACKGROUND: The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on the cross-correlation technique that can identify periodic regions in DNA sequences. RESULTS: The method reduces the dependency of window length on identification accuracy. The proposed algorithm is applied to different eukaryotic datasets and the output results are compared with those of other established methods. The proposed method increased the accuracy of exon detection by 4% to 41% relative to the most common digital signal processing methods for exon prediction. CONCLUSIONS: We demonstrated that periodic signals can be estimated using cross-correlation. In addition, discrete wavelet transform (DWT) can minimise noise while maintaining the signal. The proposed algorithm, which combines cross-correlation and DWT, significantly increases the accuracy of exonic region identification.

SUBMITTER: Abbasi O

PROVIDER: S-EPMC3306003 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform.

Abbasi Omid O Rostami Ali A Karimian Ghader G

BMC bioinformatics 20111103

<h4>Background</h4>The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on the cross-correlation technique that can identify periodic regions in DNA sequences.<h4>Results</h4>The method reduces the dependency of window length on identification accur ...[more]

PMID: 22050630

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Project description:Speech enhancement algorithms are applied in multiple levels of enhancement to improve the quality of speech signals under noisy environments known as multi-channel speech enhancement (MCSE) systems. Numerous existing algorithms are used to filter noise in speech enhancement systems, which are typically employed as a pre-processor to reduce noise and improve speech quality. They may, however, be limited in performing well under low signal-to-noise ratio (SNR) situations. The speech devices are exposed to all kinds of environmental noises which may go up to a high-level frequency of noises. The objective of this research is to conduct a noise reduction experiment for a multi-channel speech enhancement (MCSE) system in stationary and non-stationary environmental noisy situations with varying speech signal SNR levels. The experiments examined the performance of the existing and the proposed MCSE systems for environmental noises in filtering low to high SNRs environmental noises (-10 dB to 20 dB). The experiments were conducted using the AURORA and LibriSpeech datasets, which consist of different types of environmental noises. The existing MCSE (BAV-MCSE) makes use of beamforming, adaptive noise reduction and voice activity detection algorithms (BAV) to filter the noises from speech signals. The proposed MCSE (DWT-CNN-MCSE) system was developed based on discrete wavelet transform (DWT) preprocessing and convolution neural network (CNN) for denoising the input noisy speech signals to improve the performance accuracy. The performance of the existing BAV-MCSE and the proposed DWT-CNN-MCSE were measured using spectrogram analysis and word recognition rate (WRR). It was identified that the existing BAV-MCSE reported the highest WRR at 93.77% for a high SNR (at 20 dB) and 5.64% on average for a low SNR (at -10 dB) for different noises. The proposed DWT-CNN-MCSE system has proven to perform well at a low SNR with WRR of 70.55% and the highest improvement (64.91% WRR) at -10 dB SNR.

Project description:Background To evaluate the electroretinogram waveform in autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) using a discrete wavelet transform (DWT) approach. Methods A total of 55 ASD, 15 ADHD and 156 control individuals took part in this study. Full field light-adapted electroretinograms (ERGs) were recorded using a Troland protocol, accounting for pupil size, with five flash strengths ranging from –0.12 to 1.20 log photopic cd.s.m–2. A DWT analysis was performed using the Haar wavelet on the waveforms to examine the energy within the time windows of the a- and b-waves and the oscillatory potentials (OPs) which yielded six DWT coefficients related to these parameters. The central frequency bands were from 20–160 Hz relating to the a-wave, b-wave and OPs represented by the coefficients: a20, a40, b20, b40, op80, and op160, respectively. In addition, the b-wave amplitude and percentage energy contribution of the OPs (%OPs) in the total ERG broadband energy was evaluated. Results There were significant group differences (p < 0.001) in the coefficients corresponding to energies in the b-wave (b20, b40) and OPs (op80 and op160) as well as the b-wave amplitude. Notable differences between the ADHD and control groups were found in the b20 and b40 coefficients. In contrast, the greatest differences between the ASD and control group were found in the op80 and op160 coefficients. The b-wave amplitude showed both ASD and ADHD significant group differences from the control participants, for flash strengths greater than 0.4 log photopic cd.s.m–2 (p < 0.001). Conclusion This methodological approach may provide insights about neuronal activity in studies investigating group differences where retinal signaling may be altered through neurodevelopment or neurodegenerative conditions. However, further work will be required to determine if retinal signal analysis can offer a classification model for neurodevelopmental conditions in which there is a co-occurrence such as ASD and ADHD.

Dataset Information

Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform.

Publications

Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform.

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