Length distribution of sequencing by synthesis: fixed flow cycle model

DOI10.1007/S00285-012-0556-3zbMATH Open1268.05010arXiv1411.2548OpenAlexW2054003321WikidataQ45732368 ScholiaQ45732368MaRDI QIDQ353071FDOQ353071

Yong Kong

Publication date: 12 July 2013

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles under the general conditions where the nucleotide incorporation is probabilistic and may be incomplete, as in some single-molecule sequencing technologies. Unlike the previous model, the new model yields the probability distribution for the sequence length. Explicit closed form formulas are derived for the mean and variance of the distribution.

Full work available at URL: https://arxiv.org/abs/1411.2548

Recommendations

• Distributions of positive signals in pyrosequencing
• Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing
• Model-based quality assessment and base-calling for second-generation sequencing data
• Random Covering of Multiple One-Dimensional Domains with an Application to DNA Sequencing
• Probabilistic modeling and analysis of DNA fragmentation

zbMATH Keywords

generating functionprobability distributionsequence analysisnext-generation sequencingfixed flow cycle modelnucleotide incorporationsequence lengthssequencing by synthesis

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Exact enumeration problems, generating functions (05A15) Combinatorial probability (60C05)

Cites Work

• Generatingfunctionology

Cited In (1)

• Distributions of positive signals in pyrosequencing

This page was built for publication: Length distribution of sequencing by synthesis: fixed flow cycle model

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q353071)