Accuracy Assessment of Diploid Consensus Sequences
Abstract
If the origins of fragments are known in genome sequencing projects, it is straightforward to reconstruct diploid consensus sequences. In reality, however, this is not true. Although there are proposed methods to reconstruct haplotypes from genome sequencing projects, an accuracy assessment is required to evaluate the confidence of the estimated diploid consensus sequences. In this paper, we define the confidence score of diploid consensus sequences. It requires the calculation of the likelihood of an assembly. To calculate the likelihood, we propose a linear time algorithm with respect to the number of polymorphic sites. The likelihood calculation and confidence score are used for further improvements of haplotype estimation in two directions. One direction is that low-scored phases are disconnected. The other direction is that, instead of using nominal frequency 1/2, the haplotype frequency is estimated to reflect the actual contribution of each haplotype. Our method was evaluated on the simulated data whose polymorphism rate (1.2 percent) was based on Ciona intestinalis. As a result, the high accuracy of our algorithm was indicated: The true positive rate of the haplotype estimation was greater than 97 percent.
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Self-citation
- Authors
- Kim, J., Waterman, M., & Li, L.
- Affiliations
- University of Southern California (US)
- Venue
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- Published
- 2007-01
- Volume
- 4
- Issue
- 1
- Pages
- 88-97
- ISSN
- 1545-5963 (ISSN-L)
- OpenAlex
- W2069052523
- Cited by
- 11
- References
- 16
- Citations by year
- 2022: 1 · 2017: 1 · 2015: 1 · 2014: 1 · 2013: 1
- FWCI
- 0.53
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- IEEE Transactions on Computational Biology and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy
- University of Southern California
- Joint Genome Institute
- National Human Genome Research Institute (P50HG002790)
- National Institute of General Medical Sciences (R01GM075308, R01 GM75308-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- haplotype estimation, confidence scores, likelihood computation, linear-time algorithms, polymorphic sites, haplotype frequency estimation, phase assignment, Ciona intestinalis
- MeSH terms
- Algorithms, Animals, Ciona intestinalis, Computer Simulation, Diploidy, Gene Frequency, Haplotypes, Markov Chains, Polymorphism, Genetic, Probability, Models, Statistical, Likelihood Functions, Consensus Sequence, Sequence Analysis, DNA, Computational Biology
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