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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
SVC: structured visualization of evolutionary sequence conservation
S Roepcke1, P Fiziev, P H Seeburg
1Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. roepcke@molgen.mpg.de
Nucleic Acids Research
|July 2, 2005
Summary
We created a web tool to visualize evolutionary sequence conservation in vertebrate genes. This helps identify conserved gene structures and mRNA editing sites by analyzing sequence similarity.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Understanding evolutionary conservation of gene structures is crucial for deciphering gene function and regulation.
- Complex vertebrate genes exhibit intricate structures, including alternative splicing, posing challenges for comparative analysis.
- Identifying conserved non-coding elements and regulatory regions requires sophisticated visualization tools.
Purpose of the Study:
- To develop and present a web application for detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes.
- To provide a tool that integrates sequence alignment, gene structure mapping, and conservation analysis.
- To facilitate the identification of conserved features, including splice patterns and mRNA editing sites.
Main Methods:
- Development of a web application (SVC server) for analyzing orthologous gene pairs.
- Alignment of protein-coding sequences and mapping back to genomic exons to establish a gene structure scaffold.
- Analysis and visualization of sequence similarity within exons and introns, embedded into the gene structure scaffold.
Main Results:
- Emergence of a conserved gene structure scaffold from aligned orthologous genes.
- Detailed visualization of evolutionarily conserved features and complex splice patterns.
- Successful application in delineating mRNA editing sites due to high conservation in flanking exonic and intronic sequences.
Conclusions:
- The developed SVC web application effectively visualizes evolutionary sequence conservation in complex vertebrate genes.
- The tool aids in understanding gene structure, splice variations, and identifying functional elements like mRNA editing sites.
- SVC provides a valuable resource for evolutionary genomics research and functional annotation of vertebrate genes.
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