PMID: 9541874May 16, 1998Paper

Expectation and variance of true and false fragment matches in DNA restriction mapping

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
A F SiegelG van den Engh

Abstract

Consider a DNA mapping project in which overlap of clones is inferred from multiple complete restriction enzyme digests. Each enzyme cuts each clone randomly into fragments whose lengths are determined with some error. Clones that share fragments with matching lengths could contain a region of overlap. However, common fragment lengths may be due to random coincidence leading to a false overlap declaration. Although the probability of false fragment matching is small, a mapping project involves a large number of clone comparisons. Consequently, erroneous fragment matches can be a serious problem. We use a geometrical probability approach to develop exact integral formulas and first-order approximations for the expected number and variance of classes of fragment pairs that will be identified falsely as matching. We also find exact formulas for the expected value, and variance of the number of true fragment matches. These formulas are useful in comparing different mapping strategies.

References

Jan 1, 1975·Annual Review of Biochemistry·D Nathans, H O Smith
Jan 1, 1991·Bulletin of Mathematical Biology·D J Balding, D C Torney
Oct 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·M V OlsonT Frank
Mar 1, 1994·Bulletin of Mathematical Biology·S S Skiena, G Sundaram
Dec 1, 1995·Genome Research·J C Roach
Oct 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·A CoulsonJ Karn

❮ Previous
Next ❯

Citations

Jul 19, 2000·Genome Research·J C RoachA F Siegel
Dec 5, 2014·Genome Medicine·Gustavo GlusmanJared C Roach
May 16, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·A F SiegelG van den Engh

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
A F SiegelG van den Engh
Proceedings of the National Academy of Sciences of the United States of America
M Q Zhang, T G Marr
© 2022 Meta ULC. All rights reserved