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Updated: Jun 5, 2026
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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
RISCI--Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive
1Centre for Cellular and Molecular Biology, Hyderabad, India. vipin@ccmb.res.in
BMC Bioinformatics
|December 28, 2010
Summary
A new computational tool, RISCI, identifies differences in transposable element insertions and associated sequence changes between genomes. This aids in understanding evolutionary divergence and discovering novel genetic variations.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Transposable elements (TEs) are mobile genetic sequences present in genomes.
- Identifying fixed and polymorphic TE insertions aids phylogenetic and forensic analyses.
- TE insertions are often accompanied by various sequence alterations, complicating their study.
Purpose of the Study:
- To develop an automated platform for identifying differential transposable element insertions and associated sequence changes.
- To provide a tool for comparative genomics analysis of transposons across related species.
Main Methods:
- Developed RISCI (Repeat Induced Sequence Changes Identifier), a comparative genomics pipeline.
- Utilized in silico subtractive hybridization and specific alignment signatures.
- Applied the pipeline to analyze transposon insertions in human, chimpanzee, and Mycobacterium tuberculosis genomes.
Main Results:
- RISCI identified novel polymorphisms in L1HS and AluYa5 retrotransposons between human and chimpanzee genomes.
- The tool detected numerous insertion and post-insertion sequence changes.
- RISCI demonstrated versatility by analyzing IS 6100 insertion polymorphism in Mycobacterium tuberculosis strains.
Conclusions:
- RISCI effectively identifies differential TE insertions and associated sequence changes using comparative genomics.
- The pipeline is generic and applicable to various transposons and highly similar genomes.
- Large-scale comparisons using RISCI can reveal critical evolutionary events driving species divergence.
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