Human Y-chromosome gene classification using Fractal Dimension&Shannon Entropy
نویسندگان
چکیده
All genes on the human Y-chromosome were studied using fractal dimension and Shannon entropy. Clear outlier clusters were identified. Among these were 6 sequences that have since been withdrawn as CDSs and 1 additional sequence that is not in the current assembly. A methodology for ranking the sequences based on deviation from average values of FD and SE was developed. The group of sequences scored among the 10% largest deviations had abnormally high likelihood to be from centromeric or pseudoautosomal regions and low likelihood to be from X-chromosome transposed regions. lncRNA sequences were also enriched among the outliers. In addition, the number of expressed genes previously identified for evolutionary study tended to not have large deviations from the average.
منابع مشابه
Fractal Analysis of 16S rRNA Gene Sequences in Archaea Thermophiles
A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles w...
متن کاملGene Entropy-Fractal Dimension Informatics with Application to Mouse-Human Translational Medicine
DNA informatics represented by Shannon entropy and fractal dimension have been used to form 2D maps of related genes in various mammals. The distance between points on these maps for corresponding mRNA sequences in different species is used to study evolution. By quantifying the similarity of genes between species, this distance might be indicated when studies on one species (mouse) would tend ...
متن کاملScaling properties and entropy of long-range correlated time series
We calculate the Shannon entropy of a time series by using the probability density functions of the characteristic sizes of the long-range correlated clusters introduced in [A. Carbone, G. Castelli, H.E. Stanley, Phys. Rev. E 69 (2004) 026105]. We define three different measures of the entropy related, respectively, to the length, the duration and the area of the clusters. For all the three cas...
متن کاملApplication of Entropy and Fractal Dimension Analyses to the Pattern Recognition of Contaminated Fish Responses in Aquaculture
The objective of the work was to develop a non-invasive methodology for image acquisition, processing and nonlinear trajectory analysis of the collective fish response to a stochastic event. Object detection and motion estimation were performed by an optical flow algorithm in order to detect moving fish and simultaneously eliminate background, noise and artifacts. The Entropy and the Fractal Di...
متن کاملFractal Dimension Analysis of EEG Time Series Signal Buried in Random Noise
The presence of correlated randomness in EEG time series signal buried in random noise was analyzed with the Higuchi fractal algorithm. The signal recognition algorithm design was built on the fact that the theoretical fractal dimension value of 2 is an indicator for a white noise time series and correlated randomness would alter the fractal dimension value from 2. However, the limited number o...
متن کامل