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

Abstract

BackgroundWhole-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.MethodsThe 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.ResultsAs 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.ConclusionsFrom 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13323-015-0027-x) contains supplementary material, which is available to authorized users.

Isolation and characterization of SSR and EST‐SSR loci in Chamaecyparis formosensis (Cupressaceae)

“…Clean reads were assembled and merged into a single sequence 1,197,968 bp in length using Geneious version 10.2.3 (Biomatters Ltd., Auckland, New Zealand). pSTR Finder (Lee et al., 2015) was used to screen the EST‐SSR sequences, and at least five di‐, tri‐, tetra‐, penta‐, and hexanucleotide repeats were subsequently selected to generate a total of 112 potential EST‐SSR sequences.…”

Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER)

“…The long-recognized sequence variation in repeat units and flanking regions [4,5,44,45] was hitherto only rarely studied at the population level (e.g., [46]) until massively parallel sequencing techniques (MPS) recently provided access to this information (e.g., [47][48][49][50][51][52]). It was demonstrated that sequencing of STRs increases the overall discrimination power compared to that of electrophoretic sizing and offers additional advantages to forensic human identification (summarized in [53]).…”

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data

“…Though GMATo (Genome-wide Microsatellite Analyzing Tool) tool is powerful and can mine microsatellite of any genome size along with information on statistical distribution of microsatellite in the genome (Wang et al, 2013) but can neither design primers nor detect polymorphism. Though pSTR Finder (Lee et al, 2015) can identify putative polymorphic STR loci using whole genome sequence and compare two genomes in fasta format but result is without allele size and position needed for genotyping/multiplexing. CandiSSR (Xia et al, 2016) is a pipeline to identify candidate polymorphic SSRs based on the multiple assembled sequences of transcriptome/set of genome of a given species or genus but has limitation of standalone mode, complex linux/unix based system besides dependency of other requirements like MISA, Primer3, ClustalW and issues of runtime.…”