DFA7, a New Method to Distinguish between Intron-Containing and Intronless Genes

Yu, Chenglong; Deng, Minghua; Zheng, Lu; He, Rong; Yang, Jie; Yau, Stephen S.-T.

doi:10.1371/journal.pone.0101363

Cited by 14 publications

(8 citation statements)

References 27 publications

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“…According to previous studies in different mammalian species, these types of genes may experience quite different evolutionary rates than genes with an exon–intron organization ( Shabalina et al. 2010 ; Yu et al. 2014 ).…”

Section: Resultsmentioning

confidence: 99%

Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution

Valente

Álvarez

Marques

et al. 2018

Genome Biology and Evolution

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Taste perception is crucial in monitoring food intake and, hence, is thought to play a significant role in human evolution. To gain insights into possible adaptive signatures in genes encoding bitter, sweet, and umami taste receptors, we surveyed the available sequence variation data from the 1000 Genomes Project Phase 3 for TAS1R (TAS1R1-3) and TAS2R (TAS2R16 and TAS2R38) families. Our study demonstrated that genes from these two families have experienced contrasting evolutionary histories: While TAS1R1 and TAS1R3 showed worldwide evidence of positive selection, probably correlated with improved umami and sweet perception, the patterns of variation displayed by TAS2R16 and TAS2R38 were more consistent with scenarios of balancing selection that possibly conferred a heterozygous advantage associated with better capacity to perceive a wide range of bitter compounds. In TAS2R16, such adaptive events appear to have occurred restrictively in mainland Africa, whereas the strongest evidence in TAS2R38 was detected in Europe. Despite plausible associations between taste perception and the TAS1R and TAS2R selective signatures, we cannot discount other biological mechanisms as driving the evolutionary trajectories of those TAS1R and TAS2R members, especially given recent findings of taste receptors behaving as the products of pleiotropic genes involved in many functions outside the gustatory system.

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Section: Resultsmentioning

confidence: 99%

Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution

Valente

Álvarez

Marques

et al. 2018

Genome Biology and Evolution

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show abstract

“…Different from linear discriminant functions, non-liner kernels have complex discriminant functions for complicated data examples. Usually, classical non-linear kernels designed for particular applications, including polynomial kernels [76], Gaussian kernels [79,80], spectrum kernels [81], weighted degree (WD) kernels [74], WD kernels with shifts [82], string kernels [83,84], Oligo kernels [85], convolutional kernels [86], and so forth, can be used for modeling more complex decision boundaries in predicting various signal sensors [72,74,87].…”

Section: Support Vector Machines and Kernel Methodsmentioning

confidence: 99%

“…The second stage is used to select the most effective subset for the classification task, where an evolutionary feature selection algorithm reduces the set of constructed features. The Z-curve [96], a 3-D curve that provides a unique representation for the visualization and analysis of a DNA sequence [31], is used to generate new features to feed the SVM for delineating the long-range correlations in genes that contain introns [79].…”

Section: Support Vector Machines and Kernel Methodsmentioning

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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“…But these representational curves may degenerate, or may be not one-to-one mapping from DNA sequences. In order to overcome these defects, many new curves were introduced [11]- [19], while some new cluster methods were considered [20] [21] [22]. Some other representations were applied to the protein sequences [23] [24] [25] [26].…”

Section: Journal Of Applied Mathematics and Physicsmentioning

confidence: 99%

A New Numerical Method for DNA Sequence Analysis Based on 8-Dimensional Vector Representation

Zhang¹

2019

JAMP

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Background: The multiple sequence alignment (MSA) algorithms are the traditional ways to compare and analyze DNA sequences. However, for large DNA sequences, these algorithms require a long time computationally. Objective: Here we will propose a new numerical method to characterize and compare DNA sequences quickly. Method: Based on a new 2-dimensional (2D) graphical representation of DNA sequences, we can obtain an 8-dimensional vector using two basic concepts of probability, the mean and the variance. Results: We perform similarity/dissimilarity analyses among two real DNA data sets, the coding sequences of the first exon of beta-globin gene of 11 species and 31 mammalian mitochondrial genomes, respectively. Conclusion: Our results are in agreement with the existing analyses in our literatures. We also compare our approach with other methods and find that ours is more effective. IntroductionWith the rapid growth in biological data, how to get more information from these big data is a challenge for scientists. For this purpose, an important problem is to find a suitable way to digitize these DNA sequences so that the sequence comparison can be applied. For computational time reason, beyond the traditional multiple sequence alignment (MSA), many alignment-free sequence comparison methods were introduced, for more details, please refer to [1] [2] [3] and the references therein.

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DFA7, a New Method to Distinguish between Intron-Containing and Intronless Genes

Cited by 14 publications

References 27 publications

Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution

Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution

A Comprehensive Review of Emerging Computational Methods for Gene Identification

A New Numerical Method for DNA Sequence Analysis Based on 8-Dimensional Vector Representation

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