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

21.1K
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.
21.1K
DNA Bacteriophages01:26

DNA Bacteriophages

1.1K
Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
1.1K

You might also read

Related Articles

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

Sort by
Same author

Higher BMI is associated with vaginal microbiome alterations in women with PCOS.

Reproduction & fertility·2026
Same author

Computational prediction resolves thousands of homooligomeric phage protein structures.

bioRxiv : the preprint server for biology·2026
Same author

Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.

Bioinformatics (Oxford, England)·2026
Same author

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.

Science advances·2026
Same author

Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials.

bioRxiv : the preprint server for biology·2026
Same author

Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.

Environmental microbiome·2026
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Feb 18, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.9K

Phage Genome Annotation Using the RAST Pipeline.

Katelyn McNair1, Ramy Karam Aziz2,3, Gordon D Pusch3

  • 1Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 15, 2017
PubMed
Summary
This summary is machine-generated.

Bacteriophages (phages) have unique genome adaptations requiring specialized bioinformatics analysis. This study outlines challenges and solutions for phage genome annotation using the RAST pipeline.

Keywords:
Functional annotationGene predictionsGenome annotationPhageRAST

More Related Videos

Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

19.1K
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

10.7K

Related Experiment Videos

Last Updated: Feb 18, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.9K
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

19.1K
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

10.7K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Bacteriophages (phages) possess unique genomic features, including shorter genes and integrated tRNAs, reflecting their obligate parasitic lifestyle.
  • These adaptations present significant challenges for standard bioinformatics tools, complicating tasks like open reading frame (ORF) calling and noncoding RNA (ncRNA) identification.
  • Phage genomes require specialized analytical approaches due to their distinct evolutionary pressures and reliance on host machinery for replication.

Purpose of the Study:

  • To provide a comprehensive overview of the challenges encountered in phage genome annotation.
  • To present a roadmap for analyzing phage genomes, addressing specific bioinformatics hurdles.
  • To discuss solutions and methodologies implemented within the Rapid Annotation using Subsystems (RAST) pipeline for phage genome analysis.

Main Methods:

  • Review and discussion of established bioinformatics pipelines for genome annotation.
  • Adaptation and application of the RAST pipeline for the specific requirements of phage genome analysis.
  • Identification and categorization of common challenges in phage genome annotation, including ORF calling, ncRNA identification, and transposon detection.

Main Results:

  • Phage genome annotation is complicated by features such as short ORFs, overlapping genes, and the presence of mobile genetic elements.
  • The RAST pipeline offers a framework to address these challenges, improving the accuracy of phage genome annotation.
  • Specific strategies are discussed for handling ncRNA identification and the detection of insertion sequences within phage genomes.

Conclusions:

  • Effective phage genome annotation necessitates tailored bioinformatics approaches that account for their unique biological characteristics.
  • The RAST pipeline provides a valuable resource for researchers, offering solutions to common phage genome analysis problems.
  • Further development of specialized tools is crucial for advancing our understanding of phage biology through genomic analysis.