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Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling
The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using t...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Scientific World Journal
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385616/ https://www.ncbi.nlm.nih.gov/pubmed/22778697 http://dx.doi.org/10.1100/2012/365104 |
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author | Chang, Chun-Tien Tsai, Chi-Neu Tang, Chuan Yi Chen, Chun-Houh Lian, Jang-Hau Hu, Chi-Yu Tsai, Chia-Lung Chao, Angel Lai, Chyong-Huey Wang, Tzu-Hao Lee, Yun-Shien |
author_facet | Chang, Chun-Tien Tsai, Chi-Neu Tang, Chuan Yi Chen, Chun-Houh Lian, Jang-Hau Hu, Chi-Yu Tsai, Chia-Lung Chao, Angel Lai, Chyong-Huey Wang, Tzu-Hao Lee, Yun-Shien |
author_sort | Chang, Chun-Tien |
collection | PubMed |
description | The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. |
format | Online Article Text |
id | pubmed-3385616 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | The Scientific World Journal |
record_format | MEDLINE/PubMed |
spelling | pubmed-33856162012-07-09 Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling Chang, Chun-Tien Tsai, Chi-Neu Tang, Chuan Yi Chen, Chun-Houh Lian, Jang-Hau Hu, Chi-Yu Tsai, Chia-Lung Chao, Angel Lai, Chyong-Huey Wang, Tzu-Hao Lee, Yun-Shien ScientificWorldJournal Research Article The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. The Scientific World Journal 2012-06-18 /pmc/articles/PMC3385616/ /pubmed/22778697 http://dx.doi.org/10.1100/2012/365104 Text en Copyright © 2012 Chun-Tien Chang et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Chang, Chun-Tien Tsai, Chi-Neu Tang, Chuan Yi Chen, Chun-Houh Lian, Jang-Hau Hu, Chi-Yu Tsai, Chia-Lung Chao, Angel Lai, Chyong-Huey Wang, Tzu-Hao Lee, Yun-Shien Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling |
title | Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling |
title_full | Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling |
title_fullStr | Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling |
title_full_unstemmed | Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling |
title_short | Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling |
title_sort | mixed sequence reader: a program for analyzing dna sequences with heterozygous base calling |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385616/ https://www.ncbi.nlm.nih.gov/pubmed/22778697 http://dx.doi.org/10.1100/2012/365104 |
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