Polymorphic Short Tandem Repeats Finder

Welcome to pSTR Finder - A rapid method to discover polymorphic STR markers from genome-wide sequences

Microsatellites, also known as simple sequence repeat (SSR) or short tandem repeat (STR) loci, are abundant in eukaryotic genomes. Their polymorphic nature makes them suitable for use in population biology, especially in forensic science and parentage testing. The search for polymorphic STR loci can be laborious and time-consuming using conventional means for any species for which little genome sequence is known. The advent of next-generation sequencing technology has led to the development of a number of search tools for identifying STR loci. Despite recent developments it is a far from simple task to identify polymorphic STR loci from sequence data. This process is still labor intensive and few software programs are available to assist with identifying whether putative STR loci are polymorphic. Additionally it is often very difficult, if not impossible, to detect all potential STR sequences in the whole genome.

pSTR Finder (pSTR) is a web tool to efficiently analyse multiple genome sequence samples for the presence of STR loci using Tandem Repeats Finder (TRF) and generates identical, polymorphic, and different STR loci for each comparison between two samples. Currently pSTR expects sample data in the FASTA format and utilizes TRF to generate a collection of STR for each sample. pSTR will then analyse the STR from all participating samples to discover and record polymorphic STR loci, regardless of whether a sample was complete, or fractions of, a genome. We have found this program to be highly efficient when screening for potential polymorphic STR loci from genome-wide sequences and a major improvement on the current situation such that polymorphic STR loci can be identified rapidly from a large dataset.

How to Cite pSTR

pSTR Finder: A rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences

James Chun-I Lee1, Bill Tseng1, Bing-Ching Ho2,3, Adrian Linacre4
Investig Genet. 2015;6:10.

1Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan, ROC
2Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University
3NTU Center for Genomic Medicine, College of Medicine, National Taiwan University
4School of Biological Sciences, Flinders University, Adelaide 5001, Australia