1
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Use Chou’s 5-steps rule to identify DNase I hypersensitive sites via dinucleotide property matrix and extreme gradient boosting. Mol Genet Genomics 2020; 295:1431-1442. [DOI: 10.1007/s00438-020-01711-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/11/2020] [Indexed: 01/08/2023]
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2
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Yang H, Yang W, Dao FY, Lv H, Ding H, Chen W, Lin H. A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae. Brief Bioinform 2019; 21:1568-1580. [PMID: 31633777 DOI: 10.1093/bib/bbz123] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/03/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is one of the most important driving forces of biological evolution, which is initiated by double-strand DNA breaks. Recombination has important roles in genome diversity and evolution. This review firstly provides a comprehensive survey of the 15 computational methods developed for identifying recombination hotspots in Saccharomyces cerevisiae. These computational methods were discussed and compared in terms of underlying algorithms, extracted features, predictive capability and practical utility. Subsequently, a more objective benchmark data set was constructed to develop a new predictor iRSpot-Pse6NC2.0 (http://lin-group.cn/server/iRSpot-Pse6NC2.0). To further demonstrate the generalization ability of these methods, we compared iRSpot-Pse6NC2.0 with existing methods on the chromosome XVI of S. cerevisiae. The results of the independent data set test demonstrated that the new predictor is superior to existing tools in the identification of recombination hotspots. The iRSpot-Pse6NC2.0 will become an important tool for identifying recombination hotspot.
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Affiliation(s)
- Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wuritu Yang
- Development and Planning Department, Inner Mongolia University, Hohhot 010021, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Hao Lin
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
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3
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i6mA-DNCP: Computational Identification of DNA N6-Methyladenine Sites in the Rice Genome Using Optimized Dinucleotide-Based Features. Genes (Basel) 2019; 10:genes10100828. [PMID: 31635172 PMCID: PMC6826501 DOI: 10.3390/genes10100828] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/22/2022] Open
Abstract
DNA N6-methyladenine (6mA) plays an important role in regulating the gene expression of eukaryotes. Accurate identification of 6mA sites may assist in understanding genomic 6mA distributions and biological functions. Various experimental methods have been applied to detect 6mA sites in a genome-wide scope, but they are too time-consuming and expensive. Developing computational methods to rapidly identify 6mA sites is needed. In this paper, a new machine learning-based method, i6mA-DNCP, was proposed for identifying 6mA sites in the rice genome. Dinucleotide composition and dinucleotide-based DNA properties were first employed to represent DNA sequences. After a specially designed DNA property selection process, a bagging classifier was used to build the prediction model. The jackknife test on a benchmark dataset demonstrated that i6mA-DNCP could obtain 84.43% sensitivity, 88.86% specificity, 86.65% accuracy, a 0.734 Matthew's correlation coefficient (MCC), and a 0.926 area under the receiver operating characteristic curve (AUC). Moreover, three independent datasets were established to assess the generalization ability of our method. Extensive experiments validated the effectiveness of i6mA-DNCP.
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4
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Liang Y, Zhang S. iDHS-DMCAC: identifying DNase I hypersensitive sites with balanced dinucleotide-based detrending moving-average cross-correlation coefficient. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:429-445. [PMID: 31117818 DOI: 10.1080/1062936x.2019.1615546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
DNase I hypersensitive sites (DHSs) are associated with regulatory DNA elements, so their good understanding is significant for both the biomedical research and the discovery of new drugs. Traditional experimental methods are laborious, time consuming and an inaccurately task to detect DHSs. More importantly, with the avalanche of genome sequences in the postgenomic age, it is highly essential to develop cost-effective computational approaches to identify DHSs. In this paper, we develop a statistical feature extraction model using the detrended moving-average cross-correlation (DMCA) coefficient descriptor based on dinucleotide property matrix generated by the 15 DNA dinucleotide properties, and this model is named iDHS-DMCAC. A 105-dimensional feature vector is constructed for a certain window on the two class imbalanced benchmark datasets, with over-sampling and support vector machine algorithms. Rigorous cross-validations indicate that our predictor remarkably outperforms the existing models in both accuracy and stability. We anticipate that iDHS-DMCAC will become a very useful high throughput tool, or at the very least, a complementary tool to the existing methods of identifying DNase I hypersensitive sites. The datasets and source codes of the proposed model are freely available at https://github.com/shengli0201/Datasets .
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Affiliation(s)
- Y Liang
- a School of Science , Xi'an Polytechnic University , Xi'an , P. R. China
| | - S Zhang
- b School of Mathematics and Statistics , Xidian University , Xi'an , P. R. China
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5
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Zhang L, Kong L. iRSpot-PDI: Identification of recombination spots by incorporating dinucleotide property diversity information into Chou's pseudo components. Genomics 2019; 111:457-464. [DOI: 10.1016/j.ygeno.2018.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/27/2018] [Accepted: 03/03/2018] [Indexed: 12/11/2022]
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6
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Liu B, Chen J, Guo M, Wang X. Protein Remote Homology Detection and Fold Recognition Based on Sequence-Order Frequency Matrix. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:292-300. [PMID: 29990004 DOI: 10.1109/tcbb.2017.2765331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein remote homology detection and fold recognition are two critical tasks for the studies of protein structures and functions. Currently, the profile-based methods achieve the state-of-the-art performance in these fields. However, the widely used sequence profiles, like position-specific frequency matrix (PSFM) and position-specific scoring matrix (PSSM), ignore the sequence-order effects along protein sequence. In this study, we have proposed a novel profile, called sequence-order frequency matrix (SOFM), to extract the sequence-order information of neighboring residues from multiple sequence alignment (MSA). Combined with two profile feature extraction approaches, top-n-grams and the Smith-Waterman algorithm, the SOFMs are applied to protein remote homology detection and fold recognition, and two predictors called SOFM-Top and SOFM-SW are proposed. Experimental results show that SOFM contains more information content than other profiles, and these two predictors outperform other state-of-the-art methods. It is anticipated that SOFM will become a very useful profile in the studies of protein structures and functions.
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7
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Zhang S, Lin J, Su L, Zhou Z. pDHS-DSET: Prediction of DNase I hypersensitive sites in plant genome using DS evidence theory. Anal Biochem 2019; 564-565:54-63. [DOI: 10.1016/j.ab.2018.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
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8
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Jani MR, Khan Mozlish MT, Ahmed S, Tahniat NS, Farid DM, Shatabda S. iRecSpot-EF: Effective sequence based features for recombination hotspot prediction. Comput Biol Med 2018; 103:17-23. [DOI: 10.1016/j.compbiomed.2018.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/07/2018] [Accepted: 10/07/2018] [Indexed: 01/19/2023]
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9
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Yang H, Qiu WR, Liu G, Guo FB, Chen W, Chou KC, Lin H. iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC. Int J Biol Sci 2018; 14:883-891. [PMID: 29989083 PMCID: PMC6036749 DOI: 10.7150/ijbs.24616] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/04/2018] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination caused by meiotic double-strand DNA breaks. In some regions the frequency of DNA recombination is relatively higher, while in other regions the frequency is lower: the former is usually called "recombination hotspot", while the latter the "recombination coldspot". Information of the hot and cold spots may provide important clues for understanding the mechanism of genome revolution. Therefore, it is important to accurately predict these spots. In this study, we rebuilt the benchmark dataset by unifying its samples with a same length (131 bp). Based on such a foundation and using SVM (Support Vector Machine) classifier, a new predictor called "iRSpot-Pse6NC" was developed by incorporating the key hexamer features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. It has been observed via rigorous cross-validations that the proposed predictor is superior to its counterparts in overall accuracy, stability, sensitivity and specificity. For the convenience of most experimental scientists, the web-server for iRSpot-Pse6NC has been established at http://lin-group.cn/server/iRSpot-Pse6NC, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
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Affiliation(s)
- Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wang-Ren Qiu
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, 333403, China
| | - Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Feng-Biao Guo
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Gordon Life Science Institute, Boston, MA 02478, USA
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10
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Zhang S, Zhuang W, Xu Z. Prediction of DNase I hypersensitive sites in plant genome using multiple modes of pseudo components. Anal Biochem 2018; 549:149-156. [DOI: 10.1016/j.ab.2018.03.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 12/25/2022]
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11
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pDHS-ELM: computational predictor for plant DNase I hypersensitive sites based on extreme learning machines. Mol Genet Genomics 2018; 293:1035-1049. [DOI: 10.1007/s00438-018-1436-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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12
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Zhang L, Kong L. iRSpot-ADPM: Identify recombination spots by incorporating the associated dinucleotide product model into Chou's pseudo components. J Theor Biol 2018; 441:1-8. [PMID: 29305179 DOI: 10.1016/j.jtbi.2017.12.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/18/2017] [Accepted: 12/24/2017] [Indexed: 10/18/2022]
Abstract
Gene recombination is a key process to produce hereditary differences. Recombination spot identification plays an important role in revealing genome evolution and promoting DNA function study. However, traditional experiments are not good at identifying recombination spot with huge amounts of DNA sequences springed up by sequencing. At present, some machine learning methods have been proposed to speed up this identification process. However, the correlations between nucleotides pairs at different positions along DNA sequence is often ignored, which reflects the important sequence order information. For this purpose, this study proposes a novel feature extraction method, called iRSpot-ADPM, based on DNA property in a given DNA sequence. 85 features are selected from the original feature set according to the weights calculated by support vector machine. Five-fold cross validation tests on two widely used benchmark datasets indicate that the proposed method outperforms its existing counterparts on the individual specificity(Spec), Matthews correlation coefficient(MCC) value and overall accuracy(OA). The experimental results show that the proposed method is effective for accurate recombination spot identification. Moreover, it is anticipated that the proposed method could be extended to other biology sequence and be helpful in future research. The datasets and Matlab source codes can be download from the URL: http://stxy.neuq.edu.cn/info/1095/1157.htm.
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Affiliation(s)
- Lichao Zhang
- School of Mathematics and Statistics, Northeastern University at Qinhuangdao, Qinhuangdao 066004, PR China.
| | - Liang Kong
- School of Mathematics and Information Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, PR China
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13
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pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine. J Theor Biol 2017; 426:126-133. [DOI: 10.1016/j.jtbi.2017.05.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/10/2017] [Accepted: 05/23/2017] [Indexed: 11/21/2022]
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14
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Liu B, Liu Y, Jin X, Wang X, Liu B. iRSpot-DACC: a computational predictor for recombination hot/cold spots identification based on dinucleotide-based auto-cross covariance. Sci Rep 2016; 6:33483. [PMID: 27641752 PMCID: PMC5027590 DOI: 10.1038/srep33483] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
Meiotic recombination presents an uneven distribution across the genome. Genomic regions that exhibit at relatively high frequencies of recombination are called hotspots, whereas those with relatively low frequencies of recombination are called coldspots. Therefore, hotspots and coldspots would provide useful information for the study of the mechanism of recombination. In this study, we proposed a computational predictor called iRSpot-DACC to predict hot/cold spots across the yeast genome. It combined Support Vector Machines (SVMs) and a feature called dinucleotide-based auto-cross covariance (DACC), which is able to incorporate the global sequence-order information and fifteen local DNA properties into the predictor. Combined with Principal Component Analysis (PCA), its performance was further improved. Experimental results on a benchmark dataset showed that iRSpot-DACC can achieve an accuracy of 82.7%, outperforming some highly related methods.
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Affiliation(s)
- Bingquan Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150080, China
| | - Yumeng Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Xiaopeng Jin
- School of Computer Science and Technology, Harbin Engineering University, Harbin, Heilongjiang 150001, China
| | - Xiaolong Wang
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.,Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.,Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
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