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TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences
Martti T Tammi1, Erik Arner, Björn Andersson
1Department of Genetics and Pathology, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.
Computer Methods and Programs in Biomedicine
|December 7, 2002
Summary
Shotgun sequence assembly struggles with repetitive DNA. A new program, TRAP, uses multiple alignments to differentiate sequencing errors from true variations in repetitive regions, improving assembly accuracy.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Shotgun sequencing is a common method for DNA assembly.
- Current assembly software faces challenges with repetitive DNA sequences.
- Distinguishing sequencing errors from biological variations in repeats is difficult.
Purpose of the Study:
- To address the limitations of existing shotgun assembly software in handling repetitive sequences.
- To introduce a novel program, Tandem Repeat Assembly Program (TRAP), for improved repetitive sequence assembly.
Main Methods:
- Development of a new shotgun assembly program named TRAP.
- Implementation of a novel multiple-alignment based analysis method.
- Focus on distinguishing single base substitutions and indels from sequencing errors in repetitive regions.
Main Results:
- TRAP demonstrates the ability to separate long repetitive regions accurately.
- The program effectively differentiates sequencing errors from true genetic variations within repeats.
- TRAP overcomes limitations of existing fragment assembly programs for highly similar repetitive data.
Conclusions:
- TRAP offers a significant advancement for assembling DNA sequences with complex repetitive elements.
- The developed software is expected to benefit the broader sequencing community by improving assembly accuracy.
- Accurate assembly of repetitive regions is crucial for comprehensive genomic analysis.