The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix.

Statistical Applications in Genetics and Molecular Biology
Lee A NewbergCharles E Lawrence

Abstract

Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality. We derive optimal sequence weights that minimize the sum of the variances of the estimators of base frequency parameters for sequences related by a phylogenetic tree. Using these we find that approaches based upon sequence weights can perform very poorly in comparison to approaches based upon a theoretically optimal maximum-likelihood method in the inference of the parameters of a position-weight matrix. Specifically, we find that among a collection of primate sequences, even an optimal sequences-weights approach is only 51% as efficient as the maximum-likelihood approach in inferences of base frequency parameters. We also show how to employ the variance estimators to obtain a greedy ordering of species for sequencing. Application of this ordering for the weighted estimators to a primate collection yields a curve with a long plateau that is not observed with maximum-likelihood estimators. This plateau indicates that the use of weighted estimators on these data seriously limits the utility of obtaining the sequences of more than two or three ad...Continue Reading

Citations

Jun 28, 2007·BMC Bioinformatics·Eric A Stone, Arend Sidow
Jun 12, 2009·The ISME Journal·Hallgerd S C EydalKarsten Pedersen
Apr 3, 2010·Archives of Virology·Laura KalinieneLidija Truncaite
May 21, 2011·Virology Journal·Hany AnanyAndrew M Kropinski
Jul 25, 2012·Archives of Virology·Tomonori InomataAkiko Kashiwagi
Mar 5, 2016·World Journal of Microbiology & Biotechnology·Sabah A A JassimHassan El-Cheikh

❮ Previous
Next ❯

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.