- •SEQ Mapper is a web-based freely available software program that is designed to search for genetic polymorphisms within a large number of reads generated by massive parallel sequencing.
- •This program is designed to perform sequence mapping between reference data and generated reads.
- •Novel and recorded micro-variants can be identified using this new program.
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.
To read this article in full you will need to make a payment
Purchase one-time access:Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
One-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:Subscribe to Forensic Science International: Genetics
Already a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
- Finding the needle in the haystack: differentiating identical twins in paternity testing and forensics by ultra-deep next generation sequencing.Forensic Sci. Int. Genet. 2014; 9: 42-46
- Evaluation of the Ion Torrent™ HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing.Forensic Sci. Int. Genet. 2014; 12: 144-154
- Forensic STR analysis using massive parallel sequencing.Forensic Sci. Int. Genet. 2012; 6: 810-818
- Second-generation sequencing of forensic STRs using the ion torrent™ HID STR 10-plex and the ion PGM™.Forensic Sci. Int. Genet. 2014; 14: 132-140
- lobSTR: a short tandem repeat profiler for personal genomes.Genome Res. 2012; 6: 1154-1162
- STRait Razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data.Forensic Sci. Int. Genet. 2013; 7: 409-417
- STR allele sequence variation: current knowledge and future issues.Forensic Sci. Int. Genet. 2015; 18: 118-130
- Binary codes capable of correcting deletions, insertions, and reversals.Sov. Phy. Dokl. 1966; 10: 707-710
- Underlying data for sequencing the mitochondrial genome with the massively parallel sequencing platform ion torrent™ PGM™.BMC Genomics. 2015; 16: S4
- Shining a light on dark sequencing: characterising errors in ion torrent PGM data.PLoS Comput. Biol. 2013; 9: e1003031
Published online: October 20, 2016
Accepted: October 13, 2016
Received in revised form: October 5, 2016
Received: March 30, 2016
© 2016 Elsevier Ireland Ltd. All rights reserved.