Deducing intracellular distributions of metabolic pathways from genomic data.
Deducing intracellular distributions of metabolic pathways from genomic data.
复制标题
DOI：
10.1007/978-1-62703-661-0_12
复制
发表时间：
2014-01-01
期刊：
影响因子：
--
通讯作者：
Kroth, Peter G
中科院分区：
文献类型：
--
作者：
Gruber, Ansgar;Kroth, Peter G
近年来，来自各种不同生物的大量基因组被测序。大多数序列数据已经公开发布，感兴趣的用户可以对其进行评估。然而，这些丰富的信息目前被没有直接参与基因组注释的科学家充分利用。这在一定程度上是因为测序、组装和自动注释可以比基因产物的细胞内定位的识别、分类和预测快得多。注释过程的这一部分仍然在很大程度上依赖于手动精选和添加上下文信息。因此，不熟悉(整个)基因组数据类型的基因组数据库用户可能会发现自己要么被海量和多层数据淹没，要么对数据缺乏意义的分析感到不满。在本章中，我们介绍了基于与已知序列的相似性来识别和表征代谢途径中涉及的酶的基因模型的程序和方法。此外，我们描述了如何使用公开可用的预测服务器来预测蛋白质的亚细胞位置，以及如何解释所获得的结果。我们描述的策略一般适用于具有原生质体的生物体，如陆地植物或绿藻。此外，我们描述了适用于那些具有次生体(例如硅藻)的藻类的策略，与植物相比，这些藻类具有不同的细胞拓扑结构和更多的细胞内间隔。
In the recent years, a large number of genomes from a variety of different organisms have been sequenced. Most of the sequence data has been publicly released and can be assessed by interested users. However, this wealth of information is currently underexploited by scientists not directly involved in genome annotation. This is partially because sequencing, assembly, and automated annotation can be done much faster than the identification, classification, and prediction of the intracellular localization of the gene products. This part of the annotation process still largely relies on manual curation and addition of contextual information. Users of genome databases who are unfamiliar with the types of data available from (whole) genomes might therefore find themselves either overwhelmed by the vast amount and multiple layers of data or dissatisfied with less-than-meaningful analyses of the data.In this chapter we present procedures and approaches to identify and characterize gene models of enzymes involved in metabolic pathways based on their similarity to known sequences. Furthermore we describe how to predict the subcellular location of the proteins using publicly available prediction servers and how to interpret the obtained results. The strategies we describe are generally applicable to organisms with primary plastids such as land plants or green algae. Additionally, we describe strategies suitable for those groups of algae with secondary plastids (for instance diatoms), which are characterized by a different cellular topology and a larger number of intracellular compartments compared to plants.