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

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...
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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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.
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.

You might also read

Related Articles

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

Sort by
Same author

Genetic Evidence of <i>Yersinia pestis</i> from the First Pandemic.

Genes·2025
Same author

Ancient Origins and Global Diversity of Plague: Genomic Evidence for Deep Eurasian Reservoirs and Recurrent Emergence.

Pathogens (Basel, Switzerland)·2025
Same author

Comparative genomics of endophytic fungi Apiospora malaysiana with related ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity.

DNA research : an international journal for rapid publication of reports on genes and genomes·2025
Same author

Preserving the Biologically Coherent Generic Concept of <i>Phytophthora</i>, "Plant Destroyer".

Phytopathology·2025
Same author

Exploring the uncharted seas: Metabolite profiling unleashes the anticancer properties of <i>Oscillatoria salina</i>.

Heliyon·2024
Same author

Tailored Bioactive Glass Coating: Navigating Devitrification Toward a Superior Implant Performance.

ACS biomaterials science & engineering·2024
Same journal

Genome-wide analysis across Indian camel populations reveals genetic distinctiveness of the Kharai camel breed.

BMC genomics·2026
Same journal

Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.

BMC genomics·2026
Same journal

From nurse bee to queen egg: RNA-seq analysis of Apis mellifera eggs shows dietary protein-dependent gene regulation.

BMC genomics·2026
Same journal

A genome-wide association study to identify the genetic loci underlying carbapenem resistance in Acinetobacter baumannii.

BMC genomics·2026
Same journal

Comparative transcriptome analysis to reveal key drought stress-responsive genes in sorghum (Sorghum bicolor (L.) Moench).

BMC genomics·2026
Same journal

Tissue identity is the dominant determinant of cross-species transferability of a porcine developmental programme.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: May 20, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Oomycete Transcriptomics Database: a resource for oomycete transcriptomes.

Sucheta Tripathy1, Tejal Deo, Brett M Tyler

  • 1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA. tsucheta@gmail.com

BMC Genomics
|July 10, 2012
PubMed
Summary
This summary is machine-generated.

The Oomycete Transcriptomics Database (OTD) offers a centralized resource for oomycete pathogen transcriptomic and EST data. It integrates legacy and next-generation sequencing data, providing a web-based browser for visualization and analysis.

More Related Videos

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates
08:59

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates

Published on: July 2, 2018

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

Related Experiment Videos

Last Updated: May 20, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates
08:59

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates

Published on: July 2, 2018

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Oomycete pathogens cause significant economic damage, necessitating advanced data analysis tools.
  • Next-generation sequencing (NGS) technologies generate vast amounts of oomycete transcriptomic data, but analysis and visualization remain challenging.
  • Existing oomycete EST databases are outdated or unavailable, creating a need for a comprehensive resource integrating legacy and new data.

Purpose of the Study:

  • To develop an integrated database and web-based browser for oomycete pathogen transcriptomic and EST data.
  • To address the limitations of existing resources by providing a centralized platform for data storage, analysis, and visualization.
  • To facilitate the study of oomycete pathogens by making diverse datasets accessible and interpretable.

Main Methods:

  • Integrated diverse transcriptomic datasets, including ABI SOLiD and Illumina NGS data, alongside Sanger EST sequences from key oomycete species (Phytophthora sojae, Hyaloperonospora arabidopsidis).
  • Developed a web-based transcriptome browser for visualizing assembled transcripts, genome mapping, expression profiling, and read coverage.
  • Implemented on-the-fly merging of EST-derived contigs and NGS-assembled transcripts to display consensus sequences.

Main Results:

  • The Oomycete Transcriptomics Database (OTD) now stores and provides access to processed NGS and EST data for oomycete pathogens and soybean.
  • The OTD browser offers a lightweight solution for visualizing raw read alignments, transcript assemblies, and quantitative expression information.
  • The database features robust query capabilities, including integration with the VBI Microbial Database and the Phytophthora Transcriptomics Database.

Conclusions:

  • The Oomycete Transcriptomics Database (OTD) serves as a valuable public resource for oomycete pathogen research.
  • The OTD browser enhances data accessibility and analysis through quantitative visualization and integrated querying.
  • Public availability of OTD at http://www.eumicrobedb.org/transcripts/ promotes broader research and discovery in oomycete genomics.