SEQ Mapper: A DNA sequence searching tool for massively parallel sequencing data
Journal
Forensic Science International: Genetics
Journal Volume
26
Pages
66-69
Date Issued
2017
Author(s)
Abstract
The development of massively parallel sequencing (MPS) has increased greatly the scale of DNA sequencing. The analysis of massive data-files from single MPS analysis can be a major challenge if examining the data for potential polymorphic loci. To aid in the analysis of both short tandem repeat (STR) and single nucleotide polymorphisms (SNP), we have designed a new program called SEQ Mapper to search for genetic polymorphisms within a large number of reads generated by MPS. This new program has been designed to perform sequence mapping between reference data and generated reads. As a proof-of-concept, sequences derived from the allelic ladders of five STR loci and data from the amelogenin locus were used as reference data sets. Detecting and recording the polymorphic nature of each STR loci was performed using four levels of search criteria: the entire STR locus spanning the two primers; the STR region plus the two primer sequences; the STR region only; and the two primers only. All the genotypes of 5 STR loci and the amelogenin gene were identified correctly using SEQ Mapper when compared to results obtained from capillary electrophoresis based on 10 test samples in this study. SEQ Mapper is a useful tool to detect STR or SNP alleles generated by MPS in both clinical medicine and forensic genetics. ? 2016 Elsevier Ireland Ltd
Subjects
Bioinformatics; Forensic science; Massively parallel sequencing; Next generation sequencing; SNP; STR
SDGs
Other Subjects
amelogenin; amelogenin; microsatellite DNA; allele; Article; capillary electrophoresis; DNA sequence; gene locus; gene mapping; genotype; human; massively parallel sequencing; polymerase chain reaction; priority journal; short tandem repeat; single nucleotide polymorphism; software; allele; genetics; high throughput sequencing; multiplex polymerase chain reaction; single nucleotide polymorphism; software; Alleles; Amelogenin; Genotype; High-Throughput Nucleotide Sequencing; Humans; Microsatellite Repeats; Multiplex Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Software
Type
journal article