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| H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids | |
| Xie, Minzhu; Wu, Qiong1; Wang, Jianxin2; Jiang, Tao3,4,5 | |
| 2016 | |
| Source Publication | BIOINFORMATICS
 |
| ISSN | 1367-4803 |
| Volume | 32Issue:24Pages:3735-3744 |
| Abstract | Motivation: Some economically important plants including wheat and cotton have more than two copies of each chromosome. With the decreasing cost and increasing read length of next-generation sequencing technologies, reconstructing the multiple haplotypes of a polyploid genome from its sequence reads becomes practical. However, the computational challenge in polyploid haplotyping is much greater than that in diploid haplotyping, and there are few related methods. Results: This article models the polyploid haplotyping problem as an optimal poly-partition problem of the reads, called the Polyploid Balanced Optimal Partition model. For the reads sequenced from a k-ploid genome, the model tries to divide the reads into k groups such that the difference between the reads of the same group is minimized while the difference between the reads of different groups is maximized. When the genotype information is available, the model is extended to the Polyploid Balanced Optimal Partition with Genotype constraint problem. These models are all NP-hard. We propose two heuristic algorithms, H-PoP and H-PoPG, based on dynamic programming and a strategy of limiting the number of intermediate solutions at each iteration, to solve the two models, respectively. Extensive experimental results on simulated and real data show that our algorithms can solve the models effectively, and are much faster and more accurate than the recent state-of-the-art polyploid haplotyping algorithms. The experiments also show that our algorithms can deal with long reads and deep read coverage effectively and accurately. Furthermore, H-PoP might be applied to help determine the ploidy of an organism. Availability and Implementation: https://github.com/MinzhuXie/H-PoPG Contact: xieminzhu@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online. |
| Subject Area | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| DOI | 10.1093/bioinformatics/btw537 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | SNP FRAGMENTS ; ACCURATE ; DISCOVERY ; ALIGNMENT ; GENOMES |
| WOS Research Area | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS ID | WOS:000399806500006 |
| Publisher | OXFORD UNIV PRESS |
| Subtype | Article |
| Publication Place | OXFORD |
| EISSN | 1460-2059 |
| Funding Organization | National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [61370172, 61232001, 61420106009] ; US National Science FoundationNational Science Foundation (NSF) [DBI-1262107] |
| Corresponding Author Email | xieminzhu@hotmail.com |
| OA | Green Published, Bronze |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/25018 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 1.Hunan Normal Univ, Coll Phys & Informat Sci, Key Lab Internet Things Technol & Applicat, Changsha 410081, Hunan, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 3.Cent S Univ, Sch Informat Sci & Engn, Changsha 410083, Hunan, Peoples R China 4.Univ Calif Riverside, Dept Comp Sci & Engn, Riverside, CA 92521 USA 5.Tsinghua Univ, TNLIST, MOE Key Lab Bioinformat, Dept Comp Sci & Technol, Beijing, Peoples R China 6.Tsinghua Univ, TNLIST, Bioinformat Div, Dept Comp Sci & Technol, Beijing, Peoples R China |
| Recommended Citation GB/T 7714 | Xie, Minzhu,Wu, Qiong,Wang, Jianxin,et al. H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids[J]. BIOINFORMATICS,2016,32(24):3735-3744. |
| APA | Xie, Minzhu,Wu, Qiong,Wang, Jianxin,&Jiang, Tao.(2016).H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids.BIOINFORMATICS,32(24),3735-3744. |
| MLA | Xie, Minzhu,et al."H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids".BIOINFORMATICS 32.24(2016):3735-3744. |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| Xie-2016-H-PoP and H（1308KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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