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An exhaustive DNA micro-satellite map of the human genome using high performance computing
Jack R Collins1, Robert M Stephens, Bert Gold
1Advanced Biomedical Computing Center, NCI-Frederick, Frederick, MD, USA.
Genomics
|June 18, 2003
Summary
We developed a fast genome analysis tool to identify simple tandem repeats (STRs). This database of STRs aids in disease association studies and identifies potential gene expansion candidates.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- The rapid increase in sequence data necessitates efficient annotation tools.
- Identifying repetitive elements like simple tandem repeats (STRs) is crucial for genomic analysis.
Purpose of the Study:
- To develop a rapid sequence comparison method for comprehensive genome annotation.
- To identify and catalog all perfect simple tandem repeats (STRs) in the human genome draft sequence.
Main Methods:
- Implemented an exact match algorithm for rapid sequence comparison without repeat masking.
- Developed a relational database to store identified STR elements (chromosome, position, length, repeat subunit).
- Made repeat flanking sequences publicly accessible online.
Main Results:
- Successfully identified all perfect simple tandem repeats (STRs) in the human genome draft.
- Documented an increased density of potentially polymorphic STR markers across the genome.
- Identified trinucleotide repeats within gene exons, including known disease-associated genes and novel candidates.
Conclusions:
- The developed method enables rapid and complete annotation of sequence data.
- The comprehensive STR database provides valuable resources for disease association studies due to high polymorphism.
- Identified novel candidate genes for triplet repeat expansion disorders, expanding our understanding of genetic disease etiology.