title: pSTR Finder: a rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences.
abstract: BACKGROUND
  Whole-genome sequencing is performed routinely as a means to identify polymorphic genetic loci such as short tandem repeat loci. We have developed a simple tool, called pSTR Finder, which is freely available as a means of identifying putative polymorphic short tandem repeat (STR) loci from data generated from genome-wide sequences. The program performs cross comparisons on the STR sequences generated using the Tandem Repeats Finder based on multiple-genome samples in a FASTA format. These comparisons generate reports listing identical, polymorphic, and different STR loci when comparing two samples.
  
  
  METHODS
  The web site http://forensic.mc.ntu.edu.tw:9000/PSTRWeb/Default has been developed as a means to identify polymorphic STR loci within complex mass genome sequences. The program was developed to generate a series of user-friendly reports.
  
  
  RESULTS
  As proof of concept for the program, four FASTA genome sequence samples of human chromosome X (AC_000155.1, CM000685.1, NC_018934.2, and CM000274.1) were obtained from GenBank and were analyzed for the presence of putative STR regions. The sequences within AC-000155.1 were used as an initial reference sequence from which there were 5443 identical and 4305 polymorphic STR loci identified using a repeat unit of 1-6 and 10 bp as the flanking sequence either side of the putative STR loci. A reliability test was used to compare five FASTA samples, which had sections of DNA sequence removed to mimic partial or fragmented DNA sequences, to determine whether pSTR Finder can efficiently and consistently find identical, polymorphic, and different STR loci.
  
  
  CONCLUSIONS
  From the mass of DNA sequence data, the project was found to reproducibly identify polymorphic STR loci and generate user-friendly reports detailing the number and location of these potential polymorphic loci. This freely available program was found to be a useful tool to find polymorphic STR within whole-genome sequence data in forensic genetic studies.
authors.affiliation: Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051 Taiwan.
authors.forename: James Chun-I
authors.initials: JC
authors.lastname: Lee
authors.affiliation: Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051 Taiwan.
authors.forename: Bill
authors.initials: B
authors.lastname: Tseng
authors.affiliation: Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051 Taiwan ; NTU Center for Genomic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051 Taiwan.
authors.forename: Bing-Ching
authors.initials: BC
authors.lastname: Ho
authors.affiliation: School of Biological Sciences, Flinders University, Adelaide, 5001 Australia.
authors.forename: Adrian
authors.initials: A
authors.lastname: Linacre
keywords: Bioinformatics; FASTA; Forensic; MASSIVE parallel sequencing; STR; TRF; Whole-genome sequences