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

Abbasi, Omid; Rostami, Ali; Karimian, Ghader

doi:10.1186/1471-2105-12-430

Cited by 37 publications

(30 citation statements)

References 19 publications

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“…Equivalent sound levels and daily maximum 41/60 and 13/76 dB A network was good correlation with the equivalent sound level (2/60) and the maximum volume (86 to 85) dB A network of care Rza' special hospital in Mashhad in 1388 and voice level of 64 dB A network is in state hospitals in Isfahan in 1389 (11,12). The difference in results may be due to differences in methods and measuring instruments.…”

Section: Discussionmentioning

confidence: 88%

Evaluating the Noise level at Qazvin University Hospital’s Intensive Care Units

Nikpey¹,

Ghalenoei²,

Variani³

et al. 2015

Biotech Health Sci

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Background: Noise at Intensive Care Units (ICU) has an adverse effect on patients and ICU staff. There are some evidences that sleep, recovery from critical illness and average background noise in hospitals as recommended by the US Environmental Protection Agency (EPA) and World Health Organization (WHO) should not exceed 30 A-weighted decibel (dBA) and peaks during night time should be less than 40 dBA. This survey was conducted to measure noise levels and their relationship with the time of the day and location in the ICU. Objectives: The objectives of this study were to measure noise levels and evaluate their relationship with time of day and location in the ICU. Materials and Methods: This cross sectional study was conducted in a public university hospital, namely Qazvin University of Medical Sciences, Qazvin, Iran. Noise levels were measured with SLM Sound level meter (model: Tes-1443) during 24 hours with the equivalent sound level (LEQ), maximum (Max) and peak sound pressure based on the ISO 9612.this tool can measure in the range of 30 to 110 dB dynamic network. While frequency A, fast time scale networks with 125 ms fast response microphones were selected. This method says that measuring point must have distance 1.5 meter from the wall at a height of 1.25 m above ground level. At the bedside of patients measurement done by 3 TES model 1353 H Tool by a Taiwanese company. Results: This survey showed that the Equivalent Sound Level (Leq) in ICU was much higher than the standard level. The Maximum Sound Level (Lmax) in most places was 84 -89 dBA and just in one measurement in the Internal ICU reached 90 dB. The average level of Leq in ICU was 70 dB. Conclusions: Equivalent noise level and Noise Criteria in ward remarkably exceeds the standards levels. This condition will be produce Dangerous circumstances for admitted patients in ward.

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Section: Discussionmentioning

confidence: 88%

Evaluating the Noise level at Qazvin University Hospital’s Intensive Care Units

Nikpey¹,

Ghalenoei²,

Variani³

et al. 2015

Biotech Health Sci

View full text Add to dashboard Cite

show abstract

“…The proposed method was compared experimentally to previously published approaches [18]: the Discrete Fourier Transform, Anti-notch filter, Asif, AMDF, average mutual information, Fourier spectrum and the Cross-correlation methods using the sequences F56F11.4. Mostly for the experiment the sequence F56F11.4 is used because it contains almost all the information of the exon and intron regions.…”

Section: Results and Dicussionsmentioning

confidence: 99%

Improved Identification of Protein Coding Region using Wavelet Transform

Singh¹,

Singh²,

Kaur³

2014

IJCA

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Identification of protein coding regions is an important topic in genomic examination. The various coding DNA modelindependent methods are used where there is an existence of specific pattern of nucleotides. These methods presume the window length required for an examination of a DNA region. The DNA model depending coding methods catches more specific features of coding DNA. The model independent methods capture universal features of coding region. We introduce a method which is independent from the window length. Therefore objective of this paper is to improve the reorganization of protein coding region using wavelet transform with improved thresholding algorithms. This novel transform is adapt to examine periodic signal components and presents the advantage of being independent of the window length. Wavelet transform has a noisy signal, for this an improved wavelet transform threshold method has been used to improve the effects of denoising. The eukaryote data sets are used to analogize the results of proposed method with other previous methods. Finally the output obtained illustrates that the proposed method gives the better results with respect to identification accuracy. This method avoids sources of errors and makes a tool for detailed probe of the nucleotide occurrence.

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“…Other improvements for short exon prediction are wavelet-based DSP techniques [29,30], which can effectively reduce the noise from surrounding non-coding regions by using a wavelet packet transform [26,31].…”

Section: Fourier Transform and Digital Signal Processingmentioning

confidence: 99%

“…The cross-correlation method is also seen as a novel methodology in genomic signal processing for 3-periodicity prediction, which can be regarded as the convolution of two functions for measuring the similarity. In [29], after a FIR band pass filter of order 8 with a central frequency of 2π/3 was applied to numerical sequences, an impulse train of 3-periodicity was multiplied with the filtered numerical sequences in order to focus on the 3-periodicity property in the exonic region, as shown in Eq. (5).…”

Section: Fourier Transform and Digital Signal Processingmentioning

confidence: 99%

A Comprehensive Review of Emerging Computational Methods for Gene Identification

2016

J Inf Process Syst

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Gene identification is at the center of genomic studies. Although the first phase of the Encyclopedia of DNA Elements (ENCODE) project has been claimed to be complete, the annotation of the functional elements is far from being so. Computational methods in gene identification continue to play important roles in this area and other relevant issues. So far, a lot of work has been performed on this area, and a plethora of computational methods and avenues have been developed. Many review papers have summarized these methods and other related work. However, most of them focus on the methodologies from a particular aspect or perspective. Different from these existing bodies of research, this paper aims to comprehensively summarize the mainstream computational methods in gene identification and tries to provide a short but concise technical reference for future studies. Moreover, this review sheds light on the emerging trends and cutting-edge techniques that are believed to be capable of leading the research on this field in the future.

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

Cited by 37 publications

References 19 publications

Evaluating the Noise level at Qazvin University Hospital’s Intensive Care Units

Evaluating the Noise level at Qazvin University Hospital’s Intensive Care Units

Improved Identification of Protein Coding Region using Wavelet Transform

A Comprehensive Review of Emerging Computational Methods for Gene Identification

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