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STRyper：一款用于微卫星基因分型和色谱图管理的macOS应用程序。

STRyper: A macOS application for microsatellite genotyping and chromatogram management.

作者信息

Peccoud Jean

机构信息

Laboratoire Écologie et Biologie des Interactions, Équipe Écologie Évolution Symbiose, Université de Poitiers, UMR CNRS 7267, Poitiers, France.

出版信息

PLoS One. 2025 Feb 20;20(2):e0318806. doi: 10.1371/journal.pone.0318806. eCollection 2025.

DOI:10.1371/journal.pone.0318806
PMID:39977418
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11841898/
Abstract

Microsatellite markers analyzed by capillary sequencing remain useful tools for rapid genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms for microsatellite genotyping that is not restricted to human genotyping. To fill this gap, I have developed STRyper, a macOS application whose source code is published under the General Public License. STRyper only uses macOS libraries, making it very lightweight, responsive, and behaving like a modern application. Its three-pane window enables easy management and viewing of chromatograms imported from FSA and HID files, the creation of size standards and of microsatellite marker panels (including bins). STRyper features powerful search capabilities (with smart folders) and a modern graphical user interface allowing, among others, the manual correction of DNA ladders and of individual genotypes by drag-and-drop. It also introduces a new way to mitigate the effect of variations in electrophoretic conditions on estimated allele sizes.

摘要

通过毛细管测序分析的微卫星标记仍然是快速基因分型和低成本研究的有用工具。这与缺乏一个不受限于人类基因分型的免费微卫星基因分型色谱图分析应用程序形成对比。为了填补这一空白，我开发了STRyper，这是一个macOS应用程序，其源代码根据通用公共许可证发布。STRyper仅使用macOS库，使其非常轻量级、响应迅速，并且表现得像一个现代应用程序。它的三窗格窗口便于管理和查看从FSA和HID文件导入的色谱图，创建大小标准和微卫星标记面板（包括bin）。STRyper具有强大的搜索功能（带有智能文件夹）和现代图形用户界面，除其他功能外，还允许通过拖放手动校正DNA阶梯和个体基因型。它还引入了一种新方法来减轻电泳条件变化对估计等位基因大小的影响。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/a879f141fa74/pone.0318806.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/f31ac65120bd/pone.0318806.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/6337ce46c670/pone.0318806.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/bd389a510ce7/pone.0318806.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/4d246d3588d4/pone.0318806.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/a879f141fa74/pone.0318806.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/f31ac65120bd/pone.0318806.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/6337ce46c670/pone.0318806.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/bd389a510ce7/pone.0318806.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/4d246d3588d4/pone.0318806.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1423/11841898/a879f141fa74/pone.0318806.g005.jpg

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本文引用的文献

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J Evol Biol. 2023 Feb;36(2):321-336. doi: 10.1111/jeb.14106. Epub 2022 Oct 26.
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A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies.
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J Fish Biol. 2022 Nov;101(5):1225-1234. doi: 10.1111/jfb.15194. Epub 2022 Aug 29.
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Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics.不浪费，不匮乏：微卫星仍然是一种用于保护遗传学的经济且信息丰富的技术。
Ecol Evol. 2021 Oct 25;11(22):15800-15814. doi: 10.1002/ece3.8250. eCollection 2021 Nov.
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Novel Method for Accurately Assessing Pull-up Artifacts in STR Analysis.短串联重复序列分析中准确评估上拉伪像的新方法。
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