Haplotype Assembly: An Information Theoretic View
| Autor: | Si, Hongbo, Vikalo, Haris, Vishwanath, Sriram |
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| Rok vydání: | 2014 |
| Předmět: | |
| Druh dokumentu: | Working Paper |
| Popis: | This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the corresponding positions on the other chromosome in a homologous pair. Information about the order of bases in a genome is readily inferred using short reads provided by high-throughput DNA sequencing technologies. In this paper, the recovery of the target pair of haplotype sequences using short reads is rephrased as a joint source-channel coding problem. Two messages, representing haplotypes and chromosome memberships of reads, are encoded and transmitted over a channel with erasures and errors, where the channel model reflects salient features of high-throughput sequencing. The focus of this paper is on the required number of reads for reliable haplotype reconstruction, and both the necessary and sufficient conditions are presented with order-wise optimal bounds. Comment: 30 pages, 5 figures, 1 tabel, journal |
| Databáze: | arXiv |
| Externí odkaz: |
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