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

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

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

Sort by
Same author

Predicted bacterial uRBSs reveal translational coupling and ribosome-mediated RBS occlusion as gene-controlling mechanisms.

microLife·2026
Same author

Generative models for antimicrobial peptide design: auto-encoders and beyond.

BioData mining·2026
Same author

Towards FAIR and federated data ecosystems for interdisciplinary research.

PLoS computational biology·2026
Same author

Binding of Glycyl-tRNA synthetase to Mengovirus RNA stimulates translation.

Nucleic acids research·2026
Same author

PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data.

Bioinformatics (Oxford, England)·2025
Same author

A single-domain response regulator activates exopolysaccharide biosynthesis by interaction with the initiating phosphoglycosyl transferase.

mBio·2025
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jun 3, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.

Jochen Blom1, Tobias Jakobi, Daniel Doppmeier

  • 1Computational Genomics, Bielefeld University, Bielefeld, Germany. jblom@cebitec.uni-bielefeld.de

Bioinformatics (Oxford, England)
|April 1, 2011
PubMed
Summary
This summary is machine-generated.

SARUMAN is a new bioinformatics tool for short-read alignment that finds all possible positions for sequencing reads. It uses graphics hardware for speed, offering exact and complete results faster than existing methods.

More Related Videos

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Related Experiment Videos

Last Updated: Jun 3, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing (NGS) technologies necessitate efficient short-read alignment for applications like whole-genome re-sequencing and transcriptome analysis.
  • Existing alignment methods often employ heuristics, leading to missed alignment positions and loss of valuable data from alternative high-scoring alignments.

Purpose of the Study:

  • To develop a novel short-read alignment approach that identifies all valid alignment positions within a specified error threshold.
  • To accelerate the alignment process by leveraging parallel processing on graphics hardware.

Main Methods:

  • Developed SARUMAN (Semiglobal Alignment of short Reads Using CUDA and NeedleMAN-Wunsch), a mapping tool.
  • Implemented CUDA for parallel computation on graphics processing units (GPUs).
  • Integrated a filter algorithm with CUDA-accelerated alignments.

Main Results:

  • SARUMAN returns all possible alignment positions and an optimal alignment for each, under a given error threshold.
  • Achieved significant speedup in read alignment, comparable or faster than existing methods for microbial genomes.
  • Provided exact, complete, and optimal alignment results.

Conclusions:

  • SARUMAN offers a complete and accurate solution for short-read alignment, overcoming limitations of heuristic and single-best-hit approaches.
  • The use of GPU acceleration enables rapid alignment of short reads, making it suitable for large-scale genomic analyses.
  • SARUMAN is accessible on standard Linux PCs equipped with CUDA-compatible graphics accelerators.