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Using the SERV Applet to Detect Tandem Repeats in DNA Sequences and to Predict Their Variability
Matthieu Legendre1, Kevin J Verstrepen
1FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
CSH Protocols
|March 2, 2011
Summary
Tandem repeats (satellite repeats) are short DNA sequences that mutate rapidly, making them useful for forensics and genotyping. The SERV applet helps identify and assess repeat variability for marker selection.
Area of Science:
- Genetics
- Bioinformatics
Background:
- Tandem repeats, or satellite repeats, are DNA sequences with high mutation rates (100-10,000x normal).
- This instability leads to variations in repeat unit numbers among individuals and species, crucial for molecular forensics and genotyping.
- However, mutation rates differ significantly across repeat loci, necessitating methods to identify suitable markers.
Purpose of the Study:
- To introduce the Sequence-Based Estimation of Repeats Variability (SERV) applet.
- To enable the identification of tandem repeats within DNA sequences.
- To estimate the variability of these identified repeats for marker selection.
Main Methods:
- The SERV applet analyzes DNA sequences to locate tandem repeats.
- It estimates the mutation rates and variability associated with different repeat loci.
Main Results:
- SERV facilitates the discovery of tandem repeats in genomic data.
- The applet provides quantitative estimates of repeat variability.
- This allows for the selection of appropriate tandem repeats as genetic markers.
Conclusions:
- The SERV applet is a valuable tool for identifying and evaluating tandem repeats.
- It aids in selecting suitable markers for genotyping and forensic applications.
- SERV can also help identify potential hypervariable functional elements within the genome.
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