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沃尔特：一种通过末端限制片段分析在线评估端粒长度的简便方法。

WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis.

作者信息

Lyčka Martin, Peska Vratislav, Demko Martin, Spyroglou Ioannis, Kilar Agata, Fajkus Jiří, Fojtová Miloslava

机构信息

Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.

National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.

出版信息

BMC Bioinformatics. 2021 Mar 22;22(1):145. doi: 10.1186/s12859-021-04064-0.

DOI:10.1186/s12859-021-04064-0
PMID:33752601
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7986547/
Abstract

BACKGROUND

Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results.

RESULTS

To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software.

CONCLUSIONS

WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER .

摘要

背景

端粒是由短串联重复序列组成的核蛋白结构，界定线性真核染色体的末端，在维持基因组稳定性方面发挥着重要作用。因此，端粒长度的测定对许多研究至关重要。在过去几年中，已经开发出了新的端粒长度分析方法，包括基于PCR或对NGS数据进行分析的方法。尽管如此，末端限制片段（TRF）方法至今仍是金标准。然而，该方法缺乏能够分析和统计评估TRF结果的普遍接受且精确的工具。

结果

为了规范TRF结果的处理，我们开发了WALTER，这是一个在线工具集，可实现快速、可重复且用户友好的分析，包括对数据的统计评估。鉴于其基于网络的特性，它提供了一种无需安装任何额外软件即可轻松访问的方式来分析TRF数据。

结论

WALTER是对目前可用的TRF扫描图像处理工具的重大升级。这个工具集能够对几乎任何TRF扫描进行快速、高度可重复且用户友好的评估，包括对数据进行内部统计评估。WALTER平台以及详细描述TRF扫描评估、提供提示和故障排除方法的用户手册，还有用于演示该软件的测试数据，可在https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER获取，其源代码可在https://github.com/mlyc93/WALTER获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/177312125597/12859_2021_4064_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/c0ef994cb4c1/12859_2021_4064_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/1e3a59811ca9/12859_2021_4064_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/7340225add25/12859_2021_4064_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/a17996490bc9/12859_2021_4064_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/177312125597/12859_2021_4064_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/c0ef994cb4c1/12859_2021_4064_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/fbbd71d724c8/12859_2021_4064_Fig2_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd0e/7986547/177312125597/12859_2021_4064_Fig7_HTML.jpg

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