• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

BISMA——用于从独特和重复序列中的单个克隆进行快速准确的亚硫酸氢盐测序数据分析。

BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences.

机构信息

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.

出版信息

BMC Bioinformatics. 2010 May 6;11:230. doi: 10.1186/1471-2105-11-230.

DOI:10.1186/1471-2105-11-230
PMID:20459626
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2877691/
Abstract

BACKGROUND

Bisulfite sequencing is a popular method to analyze DNA methylation patterns at high resolution. A region of interest is targeted by PCR and about 20-50 subcloned DNA molecules are usually analyzed, to determine the methylation status at single CpG sites and molecule resolution.

RESULTS

The BISMA (Bisulfite Sequencing DNA Methylation Analysis) software for analysis of primary bisulfite sequencing data implements sequencing data extraction and enhanced data processing, quality controls, analysis and presentation of the methylation state. It uses an improved strategy for detection of clonal molecules and accurate CpG site detection and it supports for the first time analysis of repetitive sequences.

CONCLUSIONS

BISMA works highly automated but still provides the user full control over all steps of the analysis. The BISMA software is freely available as an online tool for academic purposes for the analysis of bisulfite sequencing data from both unique and repetitive sequences http://biochem.jacobs-university.de/BDPC/BISMA/.

摘要

背景

亚硫酸氢盐测序是一种分析 DNA 甲基化模式的常用方法，具有高分辨率。通过 PCR 靶向感兴趣的区域，通常分析大约 20-50 个亚克隆 DNA 分子，以确定单个 CpG 位点和分子分辨率的甲基化状态。

结果

用于分析原始亚硫酸氢盐测序数据的 BISMA（Bisulfite Sequencing DNA Methylation Analysis）软件实现了测序数据的提取和增强的数据处理、质量控制、甲基化状态的分析和呈现。它使用了一种改进的策略来检测克隆分子和准确的 CpG 位点检测，并首次支持重复序列的分析。

结论

BISMA 高度自动化，但仍为用户提供对分析所有步骤的完全控制。BISMA 软件是一种免费的在线工具，可用于学术目的，用于分析来自独特和重复序列的亚硫酸氢盐测序数据，网址为 http://biochem.jacobs-university.de/BDPC/BISMA/。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/e02738699cfb/1471-2105-11-230-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/b910f327e620/1471-2105-11-230-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/240a995a26c5/1471-2105-11-230-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/ea891588417c/1471-2105-11-230-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/866bafa5a33d/1471-2105-11-230-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/03614bc59f79/1471-2105-11-230-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/0b34cb40e120/1471-2105-11-230-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/e02738699cfb/1471-2105-11-230-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/b910f327e620/1471-2105-11-230-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/240a995a26c5/1471-2105-11-230-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/ea891588417c/1471-2105-11-230-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/866bafa5a33d/1471-2105-11-230-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/03614bc59f79/1471-2105-11-230-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/0b34cb40e120/1471-2105-11-230-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c96/2877691/e02738699cfb/1471-2105-11-230-7.jpg

相似文献

1
BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences.BISMA——用于从独特和重复序列中的单个克隆进行快速准确的亚硫酸氢盐测序数据分析。
BMC Bioinformatics. 2010 May 6;11:230. doi: 10.1186/1471-2105-11-230.
2
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data.BSPAT：一种基于高通量亚硫酸氢盐测序数据的用于DNA甲基化共现模式分析的快速在线工具。
BMC Bioinformatics. 2015 Jul 11;16:220. doi: 10.1186/s12859-015-0649-2.
3
Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis.亚硫酸氢盐测序数据呈现与汇编（BDPC）网络服务器——一种用于DNA甲基化分析的有用工具。
Nucleic Acids Res. 2008 Mar;36(5):e34. doi: 10.1093/nar/gkn083. Epub 2008 Feb 22.
4
BSMAP: whole genome bisulfite sequence MAPping program.BSMAP：全基因组亚硫酸氢盐序列映射程序。
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.
5
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.用于离子激流测序仪上靶向扩增子亚硫酸氢盐测序的分析与可视化工具
PLoS One. 2016 Jul 28;11(7):e0160227. doi: 10.1371/journal.pone.0160227. eCollection 2016.
6
Analysis of bisulfite sequencing data from plant DNA using CyMATE.使用CyMATE分析来自植物DNA的亚硫酸氢盐测序数据。
Methods Mol Biol. 2010;631:13-22. doi: 10.1007/978-1-60761-646-7_2.
7
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.BiQ分析器：亚硫酸氢盐测序DNA甲基化数据的可视化与质量控制
Bioinformatics. 2005 Nov 1;21(21):4067-8. doi: 10.1093/bioinformatics/bti652. Epub 2005 Sep 1.
8
MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.MethylViewer：用于亚硫酸氢盐测序和甲基转移酶可及性方案（MAPit）项目的单个模板的计算分析和编辑。
Nucleic Acids Res. 2011 Jan;39(1):e5. doi: 10.1093/nar/gkq716. Epub 2010 Oct 19.
9
B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data.B-SOLANA：一种用于分析双碱基编码亚硫酸氢盐测序数据的方法。
Bioinformatics. 2012 Feb 1;28(3):428-9. doi: 10.1093/bioinformatics/btr660. Epub 2011 Dec 6.
10
Methy-Pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis.Methy-Pipe：一个用于全基因组亚硫酸氢盐测序数据分析的集成生物信息学分析流程。
PLoS One. 2014 Jun 19;9(6):e100360. doi: 10.1371/journal.pone.0100360. eCollection 2014.

引用本文的文献

1
Heat shock induces alternative polyadenylation through dynamic DNA methylation and chromatin looping.热休克通过动态DNA甲基化和染色质环化诱导可变聚腺苷酸化。
Cell Stress Chaperones. 2025 May 22;30(4):100084. doi: 10.1016/j.cstres.2025.100084.
2
Molecular Characterization and Expression of in the Sex Reversal of .XX（或XY）性反转中[具体基因或分子名称未给出]的分子特征与表达
Animals (Basel). 2025 Jan 7;15(2):122. doi: 10.3390/ani15020122.
3
In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart.

本文引用的文献

1
Dynamic changes in the human methylome during differentiation.人类甲基组在分化过程中的动态变化。
Genome Res. 2010 Mar;20(3):320-31. doi: 10.1101/gr.101907.109. Epub 2010 Feb 4.
2
Non-imprinted allele-specific DNA methylation on human autosomes.人类常染色体上印迹等位基因特异性 DNA 甲基化。
Genome Biol. 2009;10(12):R138. doi: 10.1186/gb-2009-10-12-r138. Epub 2009 Dec 3.
3
New clustering module in BDPC bisulfite sequencing data presentation and compilation web application for DNA methylation analyses.BDPC 亚硫酸氢盐测序数据分析展示和编译网络应用中的新聚类模块，用于 DNA 甲基化分析。
探寻不同组织的表观遗传特征：马肝、肺和心脏的综合组学研究。
Mamm Genome. 2024 Dec;35(4):600-620. doi: 10.1007/s00335-024-10057-0. Epub 2024 Aug 14.
4
Comparative responses to demethylating therapy in animal models of osteosarcoma.骨肉瘤动物模型对去甲基化治疗的比较反应。
Res Sq. 2024 Jun 11:rs.3.rs-4451060. doi: 10.21203/rs.3.rs-4451060/v1.
5
Allelic chromatin structure precedes imprinted expression of during neurogenesis.等位基因染色质结构先于神经发生过程中 的印迹表达。
Genes Dev. 2023 Sep 1;37(17-18):829-843. doi: 10.1101/gad.350896.123. Epub 2023 Oct 11.
6
Characterization of the dual role of Plasmodium falciparum DNA methyltransferase in regulating transcription and translation.疟原虫 DNA 甲基转移酶在转录和翻译调控中的双重作用的表征。
Nucleic Acids Res. 2023 May 8;51(8):3918-3933. doi: 10.1093/nar/gkad248.
7
Reassessment of weak parent-of-origin expression bias shows it rarely exists outside of known imprinted regions.重新评估微弱的亲本来源表达偏倚表明，它很少存在于已知印迹区域之外。
Elife. 2023 Mar 14;12:e83364. doi: 10.7554/eLife.83364.
8
ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR.ABSP：一种自动化的 R 工具，可用于从亚硫酸氢盐测序 PCR 中高效分析特定区域的 CpG 甲基化。
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btad008.
9
Adaptation of to Soybean Peptidase Inhibitors Is Associated with the Transgenerational Upregulation of Serine Peptidases.适应大豆蛋白酶抑制剂与丝氨酸蛋白酶的跨代上调有关。
Int J Mol Sci. 2022 Nov 18;23(22):14301. doi: 10.3390/ijms232214301.
10
Functional integration of a semi-synthetic azido-queuosine derivative into translation and a tRNA modification circuit.半合成叠氮基 queuosine 衍生物在翻译和 tRNA 修饰回路中的功能整合。
Nucleic Acids Res. 2022 Oct 14;50(18):10785-10800. doi: 10.1093/nar/gkac822.
Biotechniques. 2009 Sep;47(3):781-3. doi: 10.2144/000113196.
4
Human DNA methylomes at base resolution show widespread epigenomic differences.碱基分辨率下的人类DNA甲基化组显示出广泛的表观基因组差异。
Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.
5
DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution.在单碱基对和单等位基因分辨率下对21号染色体基因启动子进行DNA甲基化分析。
PLoS Genet. 2009 Mar;5(3):e1000438. doi: 10.1371/journal.pgen.1000438. Epub 2009 Mar 27.
6
DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones.通过亚硫酸氢盐转化、克隆和单个克隆测序进行DNA甲基化分析。
Methods Mol Biol. 2009;507:177-87. doi: 10.1007/978-1-59745-522-0_14.
7
Kismeth: analyzer of plant methylation states through bisulfite sequencing.Kismeth：通过亚硫酸氢盐测序分析植物甲基化状态。
BMC Bioinformatics. 2008 Sep 11;9:371. doi: 10.1186/1471-2105-9-371.
8
QUMA: quantification tool for methylation analysis.QUMA：甲基化分析定量工具
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W170-5. doi: 10.1093/nar/gkn294. Epub 2008 May 16.
9
Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis.亚硫酸氢盐测序数据呈现与汇编（BDPC）网络服务器——一种用于DNA甲基化分析的有用工具。
Nucleic Acids Res. 2008 Mar;36(5):e34. doi: 10.1093/nar/gkn083. Epub 2008 Feb 22.
10
Clustal W and Clustal X version 2.0.Clustal W和Clustal X 2.0版本
Bioinformatics. 2007 Nov 1;23(21):2947-8. doi: 10.1093/bioinformatics/btm404. Epub 2007 Sep 10.