Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

You might also read

Related Articles

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

Sort by
Same author

Antenatal Pulmonary Hypoplasia Expands the Variety of Phenotypes Associated With MED12-Related Disorders.

Prenatal diagnosis·2025
Same author

Post-Axial Polydactyly and Postnatal Pulmonary Stenosis Observed With a SPRED1 Pathogenic Variant.

Prenatal diagnosis·2025
Same author

Parental Somatic Mosaicism Detected During Prenatal Diagnosis.

Prenatal diagnosis·2024
Same author

A novel SMOC1 pathogenic homozygous variant in a fetus with mesomelia of the lower limbs, micrognathia and hypertelorism and an incidental finding of CYP21A2-related congenital adrenal hyperplasia.

Prenatal diagnosis·2023
Same author

Prenatal diagnosis of mucopolysaccharidosis type VII facilitating treatment in neonatal period.

Prenatal diagnosis·2023
Same author

Blanket bans on fossil fuels hurt women and lower-income countries.

Nature·2022
Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024
See all related articles

Related Experiment Video

Updated: Jun 10, 2026

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Cache-oblivious dynamic programming for bioinformatics.

Rezaul Alam Chowdhury1, Hai-Son Le, Vijaya Ramachandran

  • 1Center for Computational Visualization, Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712-0027, USA. shaikat@cs.utexas.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|July 31, 2010
PubMed
Summary
This summary is machine-generated.

We developed new algorithms for bioinformatics string problems like sequence alignment and RNA structure prediction. These cache-oblivious methods improve efficiency and speed, outperforming previous approaches in experiments.

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Related Experiment Videos

Last Updated: Jun 10, 2026

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Algorithm Design

Background:

  • Bioinformatics relies on efficient string algorithms for analyzing biological sequences.
  • Existing algorithms often face performance bottlenecks due to memory hierarchy limitations (cache-inefficiency).

Purpose of the Study:

  • To develop novel cache-oblivious algorithms for key bioinformatics string problems.
  • To improve both time and space complexity, and enhance cache-efficiency compared to prior methods.

Main Methods:

  • Design and implementation of cache-oblivious algorithms for: longest common subsequence, global pairwise sequence alignment, three-way sequence alignment (median), and RNA secondary structure prediction.
  • Analysis of time and space complexity.
  • Experimental evaluation comparing new algorithms against existing implementations.

Main Results:

  • Cache-oblivious algorithms matching or improving best-known time and space complexities.
  • Significant improvements in cache-efficiency demonstrated.
  • Experimental results show faster runtimes compared to previous state-of-the-art algorithms.

Conclusions:

  • Cache-oblivious algorithms offer substantial performance gains for fundamental bioinformatics problems.
  • The developed algorithms provide a more efficient computational approach for sequence analysis and RNA structure prediction.