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pSTR Finder: a rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences
James Chun-I Lee1, Bill Tseng1, Bing-Ching Ho2
1Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051 Taiwan.
Investigative Genetics
|August 7, 2015
Summary
pSTR Finder is a free tool that identifies polymorphic short tandem repeat (STR) loci in whole-genome sequencing data. It reproducibly finds and reports these genetic markers, aiding forensic genetic studies.
Area of Science:
- Genomics
- Bioinformatics
- Forensic Genetics
Background:
- Whole-genome sequencing routinely identifies genetic loci, including short tandem repeat (STR) loci.
- Identifying polymorphic STR loci is crucial for various genetic analyses.
- Existing methods may require specialized tools for efficient STR identification from large datasets.
Purpose of the Study:
- To develop and present pSTR Finder, a freely available tool for identifying putative polymorphic STR loci from whole-genome sequence data.
- To provide a user-friendly method for analyzing complex genome sequences for STR variations.
- To facilitate forensic genetic studies by enabling efficient detection of polymorphic STRs.
Main Methods:
- Developed pSTR Finder, a web-based tool accessible at http://forensic.mc.ntu.edu.tw:9000/PSTRWeb/Default.
- Utilized Tandem Repeats Finder to identify STR sequences from multiple genome samples in FASTA format.
- Performed cross-comparisons of STR sequences to identify identical, polymorphic, and different loci.
Main Results:
- Analyzed four human chromosome X FASTA samples, identifying 5443 identical and 4305 polymorphic STR loci.
- Demonstrated the tool's ability to identify STR loci with repeat units of 1-6 bp and flanking sequences of 10 bp.
- A reliability test using fragmented DNA sequences confirmed pSTR Finder's consistent performance in identifying STR loci.
Conclusions:
- pSTR Finder reproducibly identifies polymorphic STR loci from large DNA sequence datasets.
- The tool generates user-friendly reports detailing the number and location of potential polymorphic loci.
- pSTR Finder is a valuable, freely accessible resource for forensic genetic studies utilizing whole-genome sequence data.
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