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Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species
Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus identification based on statistical models, and various...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10221851/ https://www.ncbi.nlm.nih.gov/pubmed/37240714 http://dx.doi.org/10.3390/life13051069 |
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author | Bu, Mengjia Xu, Mengxuan Tao, Shentong Cui, Peng He, Bing |
author_facet | Bu, Mengjia Xu, Mengxuan Tao, Shentong Cui, Peng He, Bing |
author_sort | Bu, Mengjia |
collection | PubMed |
description | Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus identification based on statistical models, and various software have been developed and applied in this issue. Meanwhile, in our study, very low agreement (<25%) was found among the prediction results generated by different software, which was much less consistent than expected. In order to obtain the optimal protocol of SNP mining in tree species, the algorithm principles of different alignment and SNP mining software were discussed in detail. And the prediction results were further validated based on in silico and experimental methods. In addition, hundreds of validated SNPs were provided along with some practical suggestions on program selection and accuracy improvement were provided, and we wish that these results could lay the foundation for the subsequent analysis of SNP mining. |
format | Online Article Text |
id | pubmed-10221851 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-102218512023-05-28 Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species Bu, Mengjia Xu, Mengxuan Tao, Shentong Cui, Peng He, Bing Life (Basel) Article Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus identification based on statistical models, and various software have been developed and applied in this issue. Meanwhile, in our study, very low agreement (<25%) was found among the prediction results generated by different software, which was much less consistent than expected. In order to obtain the optimal protocol of SNP mining in tree species, the algorithm principles of different alignment and SNP mining software were discussed in detail. And the prediction results were further validated based on in silico and experimental methods. In addition, hundreds of validated SNPs were provided along with some practical suggestions on program selection and accuracy improvement were provided, and we wish that these results could lay the foundation for the subsequent analysis of SNP mining. MDPI 2023-04-22 /pmc/articles/PMC10221851/ /pubmed/37240714 http://dx.doi.org/10.3390/life13051069 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Bu, Mengjia Xu, Mengxuan Tao, Shentong Cui, Peng He, Bing Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species |
title | Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species |
title_full | Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species |
title_fullStr | Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species |
title_full_unstemmed | Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species |
title_short | Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species |
title_sort | evaluation of different snp analysis software and optimal mining process in tree species |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10221851/ https://www.ncbi.nlm.nih.gov/pubmed/37240714 http://dx.doi.org/10.3390/life13051069 |
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