Related Experiment Video
Updated: May 21, 2026
09:37
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
Published on: August 15, 2019
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and
Andreas Wilke1, Travis Harrison, Jared Wilkening
1Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
BMC Bioinformatics
|June 23, 2012
Summary
Metagenome analysis is limited by computation time for sequence similarity. We present a shared reference database and tools to translate similarity searches, enabling reusable computational results for large datasets.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence similarity computation is a bottleneck in metagenome analysis.
- Sharing similarity results requires a common reference to avoid recomputation.
- Standardized formats for similarity data can reduce computational burden.
Purpose of the Study:
- To develop a mechanism for maintaining a comprehensive, non-redundant protein database.
- To create tools for translating similarity search results into various annotation namespaces.
- To enable sharing of computational results for large sequence datasets.
Main Methods:
- Automated maintenance of a comprehensive protein database with quarterly releases.
- Development of tools to translate similarity searches into annotation namespaces like KEGG and GenBank.
- Creation of a common reference for sequence similarity data.
Main Results:
- A continuously updated, non-redundant protein database.
- Tools for flexible translation of similarity search outputs.
- Facilitation of data sharing and reduced computational redundancy.
Conclusions:
- The presented data and tools allow for the generation of multiple result sets from a single computation.
- Enables computational results to be shared across different research groups for large sequence datasets.
- Addresses the computational limitations in metagenome analysis through shared resources and standardized outputs.
More Related Videos
07:38Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
Published on: April 11, 2019
10:40Comprehensive 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 Concept Videos
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
03:36Genome 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.
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...