A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.

The Journal of Physical Chemistry. B
Qiyao Zhu, Tamar Schlick

Abstract

Novel RNA motif design is of great practical importance for technology and medicine. Increasingly, computational design plays an important role in such efforts. Our coarse-grained RAG (RNA-As-Graphs) framework offers strategies for enumerating the universe of RNA 2D folds, selecting "RNA-like" candidates for design, and determining sequences that fold onto these candidates. In RAG, RNA secondary structures are represented as tree or dual graphs. Graphs with known RNA structures are called "existing", and the others are labeled "hypothetical". By using simplified features for RNA graphs, we have clustered the hypothetical graphs into "RNA-like" and "non-RNA-like" groups and proposed RNA-like graphs as candidates for design. Here, we propose a new way of designing graph features by using Fiedler vectors. The new features reflect graph shapes better, and they lead to a more clustered organization of existing graphs. We show significant increases in K-means clustering accuracy by using the new features (e.g., up to 95% and 98% accuracy for tree and dual graphs, respectively). In addition, we propose a scoring model for top graph candidate selection. This scoring model allows users to set a threshold for candidates, and it incorpora...Continue Reading

References

Jan 1, 1989·Methods in Enzymology·M Zuker
Oct 1, 1989·Computers and Biomedical Research, an International Journal·S Y LeJ V Maizel
Sep 1, 1993·Biopolymers·W FontanaP Schuster
Feb 2, 1999·Journal of Molecular Biology·E Rivas, S R Eddy
Dec 6, 2001·Nature Reviews. Genetics·S R Eddy
Mar 19, 1965·Science·R W HOLLEYA ZAMIR
Feb 14, 2004·Bioinformatics·Hin Hark GanTamar Schlick
May 20, 2006·Bioinformatics·Anke Busch, Rolf Backofen
Feb 7, 2007·Gene Therapy·N S Que-Gewirth, B A Sullenger
Aug 8, 2009·Journal of Molecular Biology·Christian LaingTamar Schlick
Jul 21, 2010·Journal of Computational Chemistry·Joseph N ZadehNiles A Pierce
Nov 26, 2010·Nature Nanotechnology·Peixuan Guo
Nov 26, 2010·Cold Spring Harbor Perspectives in Biology·Ronald R Breaker
Mar 15, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Christian Laing, Tamar Schlick
Apr 26, 2011·Current Opinion in Structural Biology·Christian Laing, Tamar Schlick
Jul 17, 2014·Nature Methods·Nathan A SiegfriedKevin M Weeks
Aug 26, 2015·Nucleic Acids Research·Mai ZahranTamar Schlick
Oct 20, 2015·Journal of Molecular Biology·Naoto BabaTamar Schlick
Feb 16, 2016·Journal of Molecular Biology·Anna Marie Pyle, Tamar Schlick
Apr 30, 2016·Methods : a Companion to Methods in Enzymology·Wayne K DawsonJanusz M Bujnicki
Feb 7, 2017·Biophysical Journal·Tamar Schlick, Anna Marie Pyle
Oct 11, 2017·Journal of Molecular Biology·Swati Jain, Tamar Schlick
Apr 6, 2018·Methods : a Companion to Methods in Enzymology·Tamar Schlick
Aug 24, 2018·Nucleic Acids Research·Swati JainTamar Schlick
Apr 1, 2019·Methods : a Companion to Methods in Enzymology·Swati JainTamar Schlick
Jan 20, 2020·Biochimica Et Biophysica Acta. General Subjects·Swati JainTamar Schlick
Oct 24, 2020·Biophysical Journal·Tamar SchlickShuting Yan

❮ 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.

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.

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.

Epigenetics Insights from Twin Studies

Find the latest research on epigenetics and twin studies 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.

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.

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.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Related Papers

Journal of Wrist Surgery
David J Slutsky
Annals of Emergency Medicine
Jennifer C ChenDavid L Schriger
The Bulletin of Mathematical Biophysics
L Demetrius
© 2021 Meta ULC. All rights reserved