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Extraction, integration and analysis of alternative splicing and protein structure distributed information
Matteo D'Antonio1, Marco Masseroli
1IFOM-IEO Campus, Via Adamello 16, Milan, Italy. matteo.dantonio@ifom-ieo-campus.it
BMC Bioinformatics
|October 16, 2009
Summary
Alternative splicing influences human gene function by creating protein variants. The PASS tool integrates splicing and protein structure data, aiding research into their functional relationships.
Area of Science:
- Bioinformatics
- Genomics
- Structural Biology
Background:
- Alternative splicing affects most human genes, producing protein isoforms with minor structural differences.
- These structural similarities suggest a link between alternative splicing and protein structure.
- Investigating this link requires integrated analysis of disparate data sources.
Purpose of the Study:
- To develop a tool for automatic data extraction, integration, and analysis of human alternative splicing and protein structure.
- To facilitate the investigation of relationships between alternative splicing and protein structure.
Main Methods:
- Integrated data from Alternative Splicing Database, Ensembl, and Protein Data Bank.
- Utilized bioinformatics tools: Protein Identifier Cross-Reference, BLAST, CLUSTALW, and FeatureMap3D.
- Developed a database and Perl scripts for data management and analysis.
- Implemented a web interface for accessible analysis.
Main Results:
- Created the Alternative Splicing and Protein Structure Scrutinizer (PASS) web application.
- Established a database storing integrated splicing and protein structure data.
- Automated the analysis pipeline for generating isoform structural information.
Conclusions:
- PASS integrates and analyzes alternative splicing and protein structure data.
- The tool generates structural information for protein isoform pairs.
- Further analysis may reveal functional associations between splicing variations and protein structure differences.
Related Concept Videos
Alternative RNA Splicing
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Protein 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,...
Genome 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.
