Emerging applications of read profiles towards the functional annotation of the genome.
Emerging applications of read profiles towards the functional annotation of the genome.
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DOI：
10.3389/fgene.2015.00188
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发表时间：
2015
影响因子：
3.7
通讯作者：
Gorodkin J
中科院分区：
文献类型：
--
作者：
Pundhir S;Poirazi P;Gorodkin J
基因组的功能注释对于理解不同物种的表型复杂性是重要的。通往功能注释的道路涉及到从单个分子的实验到高通量测序（HTS）数据的大规模分析等多个挑战。HTS数据通常是为解决特定研究问题而设计的方案的结果。测序产生读段，当映射到参考基因组时，其通常导致形成不同的模式（读段谱）。这些阅读配置文件的解释是必不可少的，他们的分析有关的研究问题解决。已经在不同的抽象层次上采用了几种策略，从某种程度上的特设到更系统的阅读配置文件分析。这些包括可以比较读段概况的方法，例如，从直接（非基于序列的）比对到将模式分类为功能组。在这篇综述中，我们强调了新兴的应用程序读取配置文件的注释的非编码RNA和顺式调控元件（克雷斯），如增强子和启动子。我们还讨论了其形成背后的生物学原理。
Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles). Interpretation of these read profiles is essential for their analysis in relation to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g., from direct (non-sequence based) alignments to classification of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory elements (CREs) such as enhancers and promoters. We also discuss the biological rationale behind their formation.
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影响因子：
16
作者：
Calo, Eliezer;Wysocka, Joanna
通讯作者：
Wysocka, Joanna
DOI：
10.1093/bioinformatics/btq363
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Erhard F;Zimmer R
通讯作者：
Zimmer R
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
12.3
作者：
Erhard F;Dölken L;Jaskiewicz L;Zimmer R
通讯作者：
Zimmer R
影响因子：
7
作者：
Berezikov, Eugene;Robine, Nicolas;Lai, Eric C.
通讯作者：
Lai, Eric C.