Dataset Information

Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.

ABSTRACT: We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for computation than other currently available algorithms. We tested the algorithm using beta hemoglobin coding sequences (HBB) of 10 different species and 18 primate mitochondria genome (mtDNA) sequences.

SUBMITTER: Sarkar BK

PROVIDER: S-EPMC8249421 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.

Sarkar Bimal Kumar BK Sharma Ashish Ranjan AR Bhattacharya Manojit M Sharma Garima G Lee Sang-Soo SS Chakraborty Chiranjib C

Scientific reports 20210701 1

We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster fo ...[more]

PMID: 34211040

Similar Datasets

Project description:Digital filtering is essential for digital imaging, image recognition, and super-resolution technology. For example, the presence of noise in images captured by digital cameras causes deterioration of the image quality and image recognition rate. In order to improve the image recognition rate, noise reduction and edge preservation must be performed during preprocessing. Noise is generally reduced using low-pass filters, such as the Gaussian filter. Although they reduce noise, such filters also have the properties of blurring edge. A strong edge blur reduces the accuracy of the feature detection in image recognition. Therefore, in our previous study, a fast M-estimation Gaussian filter for images (FMGFI) was proposed as an image filter that simultaneously achieves denoising and edge preservation. In the FMGFI, the setting of the optimal basic width of the 2nd order B-spline basis functions is important for achieving simultaneous denoising and edge preservation. In this method, the optimal basic width of the FMGFI was determined not only by manually setting the basic width but also by human judgment of the filtered images. Consequently, the inability to automatically determine the optimal basic width hindered efficient denoising during image processing Therefore, in this research, we develop and propose a method that can automatically determine the optimal basic width of the FMGFI. The previously proposed method calculates using the same basic width for all the pixels over the entire image; in contrast, the proposed method calculates using the basic width automatically determined for each pixel. The experiments confirmed that the method proposed in this study achieves higher denoising and edge preservation performance than the ones used in previous research. The results also showed that it has the highest denoising performance against salt-and-pepper noise as compared to other filters: non-local mean filter, Gaussian filter, median filter, bilateral filter, adaptive bilateral filter, and FMGFI. The experimental results for the Gaussian noise sowed that the proposed method has the same denoising and edge preservation performance as the other filters in visual evaluation. From the above, the proposed method is expected to contribute to efficient denoising and improvement of image quality by using it as a preprocessing.

Dataset Information

Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.

Publications

Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets