Highlights
- •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.
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.
Keywords
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Article info
Publication history
Published online: October 20, 2016
Accepted:
October 13,
2016
Received in revised form:
October 5,
2016
Received:
March 30,
2016
Identification
Copyright
© 2016 Elsevier Ireland Ltd. All rights reserved.
