Related Experiment Video
Updated: Jun 13, 2026
09:37
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
Published on: August 15, 2019
Gene-oriented ortholog database: a functional comparison platform for orthologous loci
Meng-Ru Ho1, Chun-houh Chen, Wen-chang Lin
1Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan.
Database : the Journal of Biological Databases and Curation
|April 30, 2010
Summary
The Gene-Oriented Ortholog Database (GOOD) addresses challenges in eukaryotic ortholog identification caused by alternative splicing (AS). It uses genomic locations to cluster isoforms, improving functional annotation and comparative genomics.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- Complete genomic sequences necessitate accurate functional annotation.
- Protein sequence-based ortholog databases struggle with eukaryotic isoforms due to alternative splicing (AS).
- Existing annotation methods can be ambiguous and incomplete.
Purpose of the Study:
- To develop a database that accurately identifies orthologs in eukaryotes, accounting for alternative splicing.
- To improve functional annotation by resolving ambiguities in ortholog identification.
- To provide a clearer framework for comparative genomics and evolutionary variation analysis.
Main Methods:
- The Gene-Oriented Ortholog Database (GOOD) clusters alternative splicing (AS)-derived isoforms using genomic locations before ortholog delineation.
- GOOD associates isoforms with their genes for comprehensive ortholog information and paralog discrimination.
- Functional annotation from Gene Ontology (GO) is integrated, with GO graphs used to visualize hierarchical relationships and address term redundancy.
Main Results:
- GOOD effectively eliminates interference from alternative splicing in ortholog identification.
- The database provides clear gene-oriented ortholog information, distinguishing isoforms and paralogs.
- GOOD enhances functional annotation by presenting GO graphs, which reveal hierarchical relationships and mitigate redundancy issues.
Conclusions:
- GOOD improves the interpretation of molecular functions in model organisms.
- The database facilitates clear comparative genomic annotation across different species.
- GOOD offers a more comprehensive approach to understanding evolutionary variation at the transcription level.
Related Concept Videos
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...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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...
00:58Genomic DNA in Eukaryotes
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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.