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SIMPROT: using an empirically determined indel distribution in simulations of protein evolution
Andy Pang1, Andrew D Smith, Paulo A S Nuin
1Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada. wcpang@mail.student.cs.uwaterloo.ca
BMC Bioinformatics
|September 29, 2005
Summary
This study introduces Simprot, a novel protein sequence evolution simulator. It models amino acid substitutions and indel events, generating accurate sequence alignments for evolutionary analysis.
Area of Science:
- Computational Biology
- Bioinformatics
- Molecular Evolution
Background:
- Protein evolution models are crucial for sequence analysis and simulating artificial data.
- Existing models primarily focus on amino acid substitutions, lacking comprehensive evolutionary event simulation.
Purpose of the Study:
- To develop an advanced method for simulating protein sequence evolution.
- To incorporate insertion and deletion (indel) events alongside amino acid substitutions.
- To generate accurate sequence alignments reflecting true evolutionary relationships.
Main Methods:
- Developed a new simulation method incorporating indel events based on empirical distributions.
- Parameterized the indel model for varying evolutionary times and simulation flexibility.
- Utilized a Monte Carlo simulation strategy implemented in the C++ program Simprot.
Main Results:
- Successfully simulated protein sequence evolution, including both substitutions and indels.
- Generated simulated sequence families and true sequence alignments.
- The simulation captures evolutionary relationships between amino acids across different sequences.
Conclusions:
- Simprot is a valuable tool for testing protein sequence analysis methods.
- It aids in evaluating alignment methods, phylogenetic tree construction, and homology detection.
- The tool is essential for studies requiring knowledge of true sequence evolution pathways.