The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics
Repeat region with length of one to six base pairs (bp), found in DNA sequences is known as short tandem repeats (STRs). Currently, high-throughput next-generation sequencers have facilitated the effective polymorphic STR markers’ identification. In this study, a new whole genome STRs pipeline has...
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Malaysian Society of Applied Biology
2016
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| Online Access: | http://journalarticle.ukm.my/11816/ http://journalarticle.ukm.my/11816/ http://journalarticle.ukm.my/11816/1/45_02_12.pdf |
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ukm-118162018-07-02T01:26:58Z http://journalarticle.ukm.my/11816/ The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics Nur Nabilah A., Venkataramanan S., Repeat region with length of one to six base pairs (bp), found in DNA sequences is known as short tandem repeats (STRs). Currently, high-throughput next-generation sequencers have facilitated the effective polymorphic STR markers’ identification. In this study, a new whole genome STRs pipeline has been established in order to call and profile STRs from next-generation sequencing (NGS) data. Firstly, genome sequences of Helicobater pylori strain, CPY1124 and PeCan4 as reference genome were retrieved from European Nucleotide Archive (ENA) database which then the quality of sequences were checked using FastQC. The assembly of genome sequences was done by VELVET de novo assembler. Unordered contigs from VELVET’s output was realigned using multiple genome alignment (MAUVE) to obtain ordered contigs sequence. Lastly, STRs calling and profiling by Tandem Repeat Finder was done with the parameters of (2: match, 7: mismatch and 7: indels). These parameters are for Smith-Waterman style local alignment using wrap-around dynamic programming. As a result, this new pipeline enables to identify polymorphic and unique STRs which are GTTTG and AAACCC from CPY1124. This pipeline has been compared with other available STRs profiling pipeline like pSTR Finder and Tandem Repeat Database (TRDB) for validation purpose. The similar output producing by both tools thus indicates the reliability of this new pipeline for future usage. Malaysian Society of Applied Biology 2016-12 Article PeerReviewed application/pdf en http://journalarticle.ukm.my/11816/1/45_02_12.pdf Nur Nabilah A., and Venkataramanan S., (2016) The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics. Malaysian Applied Biology, 45 (2). pp. 75-85. ISSN 0126-8643 http://www.mabjournal.com/index.php?option=com_content&view=article&id=565&catid=59:current-view&Itemid=56 |
| repository_type |
Digital Repository |
| institution_category |
Local University |
| institution |
Universiti Kebangasaan Malaysia |
| building |
UKM Institutional Repository |
| collection |
Online Access |
| language |
English |
| description |
Repeat region with length of one to six base pairs (bp), found in DNA sequences is known as short tandem repeats (STRs).
Currently, high-throughput next-generation sequencers have facilitated the effective polymorphic STR markers’ identification.
In this study, a new whole genome STRs pipeline has been established in order to call and profile STRs from next-generation
sequencing (NGS) data. Firstly, genome sequences of Helicobater pylori strain, CPY1124 and PeCan4 as reference genome
were retrieved from European Nucleotide Archive (ENA) database which then the quality of sequences were checked using
FastQC. The assembly of genome sequences was done by VELVET de novo assembler. Unordered contigs from VELVET’s
output was realigned using multiple genome alignment (MAUVE) to obtain ordered contigs sequence. Lastly, STRs calling
and profiling by Tandem Repeat Finder was done with the parameters of (2: match, 7: mismatch and 7: indels). These
parameters are for Smith-Waterman style local alignment using wrap-around dynamic programming. As a result, this new
pipeline enables to identify polymorphic and unique STRs which are GTTTG and AAACCC from CPY1124. This pipeline
has been compared with other available STRs profiling pipeline like pSTR Finder and Tandem Repeat Database (TRDB) for
validation purpose. The similar output producing by both tools thus indicates the reliability of this new pipeline for future
usage. |
| format |
Article |
| author |
Nur Nabilah A., Venkataramanan S., |
| spellingShingle |
Nur Nabilah A., Venkataramanan S., The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics |
| author_facet |
Nur Nabilah A., Venkataramanan S., |
| author_sort |
Nur Nabilah A., |
| title |
The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics |
| title_short |
The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics |
| title_full |
The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics |
| title_fullStr |
The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics |
| title_full_unstemmed |
The profiling of short tandem repeats (STRS) fromnext-generation sequencing (NGS) data by establishing a whole genome STRS pipeline for forensic bioinformatics |
| title_sort |
profiling of short tandem repeats (strs) fromnext-generation sequencing (ngs) data by establishing a whole genome strs pipeline for forensic bioinformatics |
| publisher |
Malaysian Society of Applied Biology |
| publishDate |
2016 |
| url |
http://journalarticle.ukm.my/11816/ http://journalarticle.ukm.my/11816/ http://journalarticle.ukm.my/11816/1/45_02_12.pdf |
| first_indexed |
2023-09-18T20:01:12Z |
| last_indexed |
2023-09-18T20:01:12Z |
| _version_ |
1777406860684427264 |