Related Experiment Video
Updated: Mar 13, 2026
09:29
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
Published on: May 15, 2019
20.5K
IMG/M: integrated genome and metagenome comparative data analysis system.
I-Min A Chen1, Victor M Markowitz2, Ken Chu2
1Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA IMAChen@lbl.gov.
Nucleic Acids Research
|October 15, 2016
Summary
The Integrated Microbial Genomes with Microbiome Samples (IMG/M) database has tripled its data and expanded analysis tools. This resource supports comprehensive microbiome research with diverse genomic and metagenomic datasets.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- The Integrated Microbial Genomes with Microbiome Samples (IMG/M) system is a crucial resource for microbial genomics and microbiome research.
- It houses diverse sequence data from cultured and uncultured organisms, as well as environmental samples.
Purpose of the Study:
- To update on the growth and enhancements of the IMG/M system since its last report.
- To highlight the expanded capabilities for analyzing microbial and microbiome datasets.
Main Methods:
- Data integration from JGI, public archives, and scientist submissions.
- Utilizing JGI's genome and metagenome annotation pipelines for structural and functional analysis.
- Providing analytical and visualization tools for data exploration.
Main Results:
- IMG/M dataset content has tripled, including an increase in protein coding genes.
- Analysis tools have been enhanced to manage the growing volume and size of datasets.
- Open access for public datasets and a companion expert review system for private data are available.
Conclusions:
- IMG/M has significantly expanded its data holdings and analytical functionalities.
- The system continues to be a vital, growing resource for the microbial and microbiome research community.
- Enhanced tools support the examination of increasingly large and complex biological datasets.
Related Concept Videos
01:29Modern Molecular Taxonomy
812
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...
812
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
17.4K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
17.4K
02:54Evolutionary Relationships through Genome Comparisons
7.2K
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...
7.2K
01:24Microbial Classification System
1.5K
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...
1.5K
01:20Applications of Molecular Taxonomy
644
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...
644
00:46Genomic DNA in Prokaryotes
49.8K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic Diversity in Bacteria
Although bacterial genomes are much...
49.8K