qmotif：从全基因组序列数据中确定端粒含量
qmotif: determination of telomere content from whole-genome sequence data.
作者信息
Holmes Oliver, Nones Katia, Tang Yue Hang, Loffler Kelly A, Lee Michael, Patch Ann-Marie, Dagg Rebecca A, Lau Loretta M S, Leonard Conrad, Wood Scott, Xu Qinying, Pickett Hilda A, Reddel Roger R, Barbour Andrew P, Grimmond Sean M, Waddell Nicola, Pearson John V
机构信息
QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia.
Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia.
出版信息
Bioinform Adv. 2022 Jan 31;2(1):vbac005. doi: 10.1093/bioadv/vbac005. eCollection 2022.
MOTIVATION
Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA samples. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing.
RESULTS
qmotif shows similar results to quantitative PCR, the standard method for high-throughput clinical telomere length quantification. qmotif output correlates strongly with the output of other tools for determining telomere sequence content, TelSeq and TelomereHunter, but can run in a fraction of the time-usually under a minute.
AVAILABILITY AND IMPLEMENTATION
qmotif is implemented in Java and source code is available at https://github.com/AdamaJava/adamajava, with instructions on how to build and use the application available from https://adamajava.readthedocs.io/en/latest/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at online.
动机
在癌症中已观察到端粒长度的变化，这可能表明参与致癌作用的机制。大多数用于估计端粒长度的方法都需要对DNA样本进行实验室分析。在此，我们介绍qmotif，这是一种快速简便的工具，可直接从全基因组测序中确定端粒重复序列含量，以此作为端粒长度的估计值。
结果
qmotif的结果与定量PCR相似，定量PCR是高通量临床端粒长度定量的标准方法。qmotif的输出与其他用于确定端粒序列含量的工具（TelSeq和TelomereHunter）的输出高度相关，但运行时间仅为其几分之一，通常不到一分钟。
可用性与实现
qmotif用Java实现，源代码可在https://github.com/AdamaJava/adamajava获取，关于如何构建和使用该应用程序的说明可从https://adamajava.readthedocs.io/en/latest/获取。
补充信息
补充数据可在网上获取。
Zotero 插件