Related Experiment Video
Updated: Aug 11, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
Hanno Teeling1, Frank Oliver Gloeckner
1Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany. hteeling@mpi-bremen.de
BMC Bioinformatics
|February 16, 2006
Summary
RibAlign offers a novel database and tool for aligning ribosomal protein sequences, improving prokaryotic phylogenetic analysis beyond 16S rRNA limitations. This facilitates more accurate evolutionary relationship studies using concatenated protein sequences.
Area of Science:
- Microbiology
- Bioinformatics
- Evolutionary Biology
Background:
- 16S ribosomal RNA (rRNA) sequencing is standard for prokaryotic phylogeny but lacks resolution for higher-level relationships.
- Limited universal phylogenetic markers and information content in prokaryotic genomes necessitate improved methods.
- Concatenation of ribosomal protein sequences offers enhanced phylogenetic resolution.
Purpose of the Study:
- To develop RibAlign, a comprehensive database and tool for ribosomal protein sequence analysis.
- To address the lack of a centralized database and retrieval tool for ribosomal protein sequences.
- To facilitate improved phylogenetic reconstruction for prokaryotes.
Main Methods:
- Creation of a fast, scalable database for eubacterial ribosomal protein sequences.
- Development of semi-automatic extraction of sequences from GenBank and FASTA files.
- Implementation of import/export functions for phylogenetic software (PHYLIP, MrBayes).
Main Results:
- RibAlign provides a specialized database for ribosomal protein sequences.
- The tool enables efficient sequence retrieval, alignment, concatenation, and filtering.
- Generated files are directly compatible with major phylogenetic reconstruction programs.
Conclusions:
- RibAlign overcomes limitations in current phylogenetic methods based on concatenated ribosomal proteins.
- The tool supports the growing number of whole-genome sequencing projects.
- RibAlign is valuable for studying the phylogeny of newly discovered or underrepresented bacterial phyla.
Related Concept Videos
01:28Microbial Phylogeny
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
02:54Evolutionary Relationships through Genome Comparisons
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...
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
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...
01:23Phylogeny
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
01:29Modern 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...
03:21Phylogenetic Trees
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...