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

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...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
ER Retrieval Pathway01:45

ER Retrieval Pathway

In the secretory pathway, vesicles transport proteins from one cellular compartment to another in forward transport to deliver the protein to its correct location. Occasionally, misfolded proteins and incorrect proteins escape their original compartments, and a retrieval pathway is used to return the escaped proteins to their original compartment.
The ER uses many checkpoints to prevent the entry of incorrectly folded or a resident protein as cargo onto a transport vesicle. These mechanisms...
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.
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

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

Sort by
Same author

Peripheral blood RNA-seq analysis in bipolar and schizophrenia spectrum disorders: modest influence of antipsychotic treatment.

Frontiers in pharmacology·2026
Same author

Adverse Outcome Pathway 298: Increase in Reactive Oxygen Species Leading to Human Treatment-Resistant Gastric Cancer.

Cancers·2026
Same author

Ratio-Driven Lipoprotein Mapping Refines Genetic Pathways of Cardiometabolic Risk.

Research square·2026
Same author

Subtelomeric elements provide stability to short telomeres in telomerase-negative cells of the budding yeast Naumovozyma castellii.

Current genetics·2025
Same author

Cathelicidin LL-37-Induced Transcriptome of Human Keratinocyte Identifies Chemokine CXCL10 Link to T-Cell-Mediated Rosacea Pathogenesis through Jak1/STAT1 Pathway.

The Journal of investigative dermatology·2025
Same author

Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

Current issues in molecular biology·2025

Related Experiment Video

Updated: Jul 2, 2026

Development of Compendium for Esophageal Squamous Cell Carcinoma
03:36

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

GOfetcher: a database with complex searching facility for gene ontology.

Mehdi Pirooznia1, Tanwir Habib, Edward J Perkins

  • 1Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA. mehdi.pirooznia@usm.edu

Bioinformatics (Oxford, England)
|August 30, 2008
PubMed
Summary

GOfetcher is a new web tool that enhances Gene Ontology (GO) project searches with comprehensive facilities. It offers multiple search levels and diverse data output formats for improved ontology management and gene information retrieval.

More Related Videos

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Related Experiment Videos

Last Updated: Jul 2, 2026

Development of Compendium for Esophageal Squamous Cell Carcinoma
03:36

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Ontology Engineering

Background:

  • The Gene Ontology (GO) project requires robust tools for ontology creation, maintenance, and utilization.
  • Existing GO tools often lack comprehensive search functionalities, hindering efficient data access and analysis.
  • Developing advanced tools is crucial for the continued growth and usability of the GO project.

Purpose of the Study:

  • To introduce GOfetcher, a novel web application designed to overcome limitations in existing Gene Ontology (GO) tools.
  • To provide a comprehensive search facility for the GO project, enhancing user accessibility and data retrieval.
  • To offer versatile output formats for GO data, facilitating downstream analysis and integration.

Main Methods:

  • Development of a web application named GOfetcher.
  • Implementation of three distinct search levels: Quick Search, Advanced Search, and Upload Files.
  • Inclusion of a unique search function linking nucleotide or protein accession numbers to GO information.
  • Support for multiple data output formats, including spreadsheet, CSV, and XML.

Main Results:

  • GOfetcher provides a comprehensive search capability for the Gene Ontology (GO).
  • The application supports diverse search strategies, including accession number-based queries.
  • Results can be exported in various formats (spreadsheet, CSV, XML), increasing data utility.
  • The GOfetcher database is publicly accessible at http://mcbc.usm.edu/gofetcher/.

Conclusions:

  • GOfetcher significantly improves the searchability and usability of the Gene Ontology (GO) project.
  • The tool's comprehensive features and flexible output formats aid researchers in gene annotation and analysis.
  • GOfetcher represents a valuable contribution to the bioinformatics community for managing and accessing GO data.