Related Experiment Video

Updated: Jun 2, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

Local structural alignment of RNA with affine gap model

Thomas King-Fung Wong¹, Brenda Wing-Yan Cheung, Tak-Wah Lam

¹Department of Computer Science, The University of Hong Kong, Hong Kong. kfwong@cs.hku.hk.

BMC Proceedings

|May 11, 2011

Abstract

Background:

Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps.

Results:

In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem.

Conclusions:

Based on an experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

Related Concept Videos

Nucleic Acid Structure

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

Nucleic Acids

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

Nucleic acids

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

Articles linked to this work by shared authors, journal, and citation graph.

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Nature methods·2026

A Systematic Survey and Benchmark of Deep Learning for Molecular Property Prediction in the Foundation Model Era.

Journal of chemical theory and computation·2026

piqtree: a python package for seamless phylogenetic inference with IQ-TREE.

Molecular biology and evolution·2026

LIMA: Towards building a non-invasive and stealthy real-world adversarial attack model for traffic sign recognition systems.

Neural networks : the official journal of the International Neural Network Society·2026

Protein domain-specific genotype-phenotype correlation study of neurofibromatosis type 1.

Scientific reports·2025

Primary prevention cardiovascular disease risk prediction model for contemporary Chinese (1°P-CARDIAC): Model derivation and validation using a hybrid statistical and machine-learning approach.

PloS one·2025

See all related articles