Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods

Bioinformatics
A KelE Wingender

Abstract

Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. We developed a novel method for analysis of unaligned sets of sequences based on kernel estimation. The method is able to reveal 'multiple local patterns'-a set of weight matrices. Every weight matrix characterizes a pattern that can be found in a significant subset of sequences under analysis. The method developed has been compared with several other methods of pattern discovery such as Gibbs sampling, MEME, CONSENSUS, MULTIPROFILER and PROJECTION. The kernel method showed the best performance in terms of how close the revealed weight matrices are to the original ones. We applied the kernel method to analyze three samples of promoters (cell-cycle, T-cells and muscle-specific). We compared the multiple patterns revealed with the TRANSFAC library of weight matrices and found a strong similarity to several weight matrices for transcription factors known to be involved in the mentioned specific gene reg...Continue Reading

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

IEEE Transactions on Pattern Analysis and Machine Intelligence
Francesco Camastra, Alessandro Verri
Neural Networks : the Official Journal of the International Neural Network Society
Alex J. SmolaKlaus Robert Müller
IEEE Transactions on Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the IEEE Systems, Man, and Cybernetics Society
L X Wang, R Langari
© 2022 Meta ULC. All rights reserved