Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Evolution of Microbial Genome

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.

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

Microbial Classification System

Microbial Classification System

Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...

Rapid Identification of Pathogens

Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...

Automated Microbial Diagnostics

Automated Microbial Diagnostics

Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...

You might also read

Related Articles

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

Sort by

Same author

Humoral Immunity Profiling of Subjects with Myalgic Encephalomyelitis Using a Random Peptide Microarray Differentiates Cases from Controls with High Specificity and Sensitivity.

Molecular neurobiology·2016

Same author

Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening.

Physiologia plantarum·2013

Same author

Transcriptome and gene expression analysis in cold-acclimated guayule (Parthenium argentatum) rubber-producing tissue.

Phytochemistry·2012

Same author

What to do about data?

Bioinformation·2011

Same author

Standardizing the next generation of bioinformatics software development with BioHDF (HDF5).

Advances in experimental medicine and biology·2010

Same author

Annotating genes of known and unknown function by large-scale coexpression analysis.

Plant physiology·2008

Search research articles

Related Experiment Video

Updated: Jul 3, 2026

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

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

Published on: December 7, 2021

Specialized hidden markov model databases for microbial genomics.

Martin Gollery¹

¹University of Nevada, Reno 1664 N. Virginia Street Reno NV 89557-0014 USA.

Comparative and Functional Genomics

|July 17, 2008

Summary

This summary is machine-generated.

Hidden Markov models (HMMs) are crucial for biological sequence analysis. This paper explores HMM algorithms and databases, offering methods for creating custom HMM targets for large-scale genomic studies.

More Related Videos

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Related Experiment Videos

Last Updated: Jul 3, 2026

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

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

Published on: December 7, 2021

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Hidden Markov models (HMMs) are increasingly vital for analyzing biological sequences.
The scale of HMM databases and their application in genomics has rapidly expanded.
Current trends involve analyzing entire microbial genomes and large collections of genomes.

Purpose of the Study:

To review available HMM algorithms and databases.
To provide guidance on developing custom HMM targets.
To address the growing need for efficient HMM analysis in large-scale genomic research.

Main Methods:

Exploration of readily available HMM and HMM-like algorithms.
Review of publicly accessible HMM databases.
Outline of methodologies for custom HMM target development.

Main Results:

Identification of key HMM algorithms and databases relevant to modern biological sequence analysis.
Provision of practical strategies for users to create their own HMM targets.
Demonstration of the feasibility of applying HMMs to large-scale genomic datasets.

Conclusions:

The increasing importance of HMMs necessitates accessible tools and databases.
Developing custom HMM targets empowers researchers to tailor analyses to specific biological questions.
This work facilitates the efficient use of HMMs in the era of large-scale genome analysis.