《BIOINFORMATICS：概念基础入门》- 生物信息学初学者的优秀指南

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"《BIOINFORMATICS: A CONCEPT-BASED INTRODUCTION》是由Venkatarajan Subramanian Mathura和Pandjassarame Kangueane合著的一本适合初学者的生物信息学入门书籍，旨在为读者提供生物信息学的基础概念。" 在生物信息学这个领域，这本书被标记为一本优秀的参考资料。生物信息学是一门结合生物学、计算机科学、数学和统计学的交叉学科，用于处理和解释生物学数据，特别是基因组、蛋白质组和表观遗传学等领域的大量数据。《BIOINFORMATICS: A CONCEPT-BASED INTRODUCTION》作为一本概念导向的教材，对这个复杂的主题进行了深入浅出的讲解。书中可能涵盖了以下关键知识点： 1. 基础概念：包括生物信息学的基本定义、历史和发展，以及它在现代生命科学研究中的重要性。 2. 生物序列分析：讲解DNA、RNA和蛋白质序列的比对、搜索、分类和进化分析，如BLAST、ClustalW和Phylogenetic树构建等方法。 3. 基因组学：介绍全基因组测序技术、基因预测、功能注释和基因组组装过程。 4. 蛋白质结构与功能：讨论蛋白质结构的预测（如利用SWISS-MODEL）和功能分析，以及蛋白质-蛋白质相互作用网络的构建。 5. 生物数据库：阐述各类生物数据库（如GenBank、UniProt、KEGG）的使用和数据获取。 6. 生物统计与机器学习：探讨用于数据分析的统计模型，如线性回归、逻辑回归，以及支持向量机、神经网络等机器学习算法在生物信息学中的应用。 7. 生物信息学工具与软件：介绍常用生物信息学工具，如BEDTools、samtools、R语言及其生物信息学包，以及如何利用这些工具进行数据分析。 8. 系统生物学与网络生物学：讲解系统级别的生物学研究，如代谢途径建模和基因调控网络分析。 9. 计算生物学方法：涵盖模拟、建模和仿真技术，如蒙特卡洛方法、动力学模型等。 10. 案例研究与实际应用：通过具体的研究案例，展示生物信息学在疾病诊断、药物发现和个性化医疗等方面的应用。此外，作者Venkatarajan Subramanian Mathura和Pandjassarame Kangueane分别在Roskamp Institute和Biomed-Informatics担任科学家和管理职务，这表明书中的内容可能结合了实际研究经验，具有很高的实践价值。虽然书的具体内容没有详细给出，但根据标题和描述，可以推断本书将为初学者提供一个全面而扎实的生物信息学基础。

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Contents

14 Bioinformatics Analysis: Gene Fusion .............................................. 175

Meena Kishore Sakharkar, Yiting Yu

1. Introduction.......................................................................................175

2. Identification of Fusion Proteins.......................................................176

2.1 Human Fusion Proteins Mimicking Bacterial Operons..............177

2.2 Human Fusion Proteins Simulating Bacterial Subunit

Interfaces.....................................................................................177

2.3 Fusion Proteins Exhibiting Multiple Functions ..........................177

2.4 Fusion Proteins Showing Alternative Splicing...........................178

3. Remarks on Fusion Proteins .............................................................178

References.............................................................................................180

Index .......................................................................................................... 183

and Pandjassarame Kangueane

C.-H. Volmar et al.

of life at the cellular level. Problems at the molecular level often result in

physiological alterations that in turn affect homeostasis of the whole

organism.

The life of an organism is mapped in its genome, a long sequence of

nucleic acids that consists of the entire set of chromosomes of the organism.

Genes are a stretch of nucleic acids, which represent a functional aspect of

the genome. Each gene codes for a limited set of proteins. The same genes

may be found in very distant animals such as a cow and a jellyfish, but their

regulation (control of the activity of those genes) may be different and

appears to be of utmost importance. Cellular processes such as apoptosis or

programmed cell death are encoded within the genome of individual

organisms in a complex manner. With the recent sequencing of the human

genome, mankind has for the first time the opportunity to attempt to

understand the involvement of the genes in sequence of events involved in

the development of an organism (ontogenesis) as well as in the etiology of

various diseases. RNA is the product of the transcription of DNA and is then

translated into polypeptide, which folds into a functional form called protein.

Any mutation in DNA, if not repaired by the various polymerases, may

result in the transcription of faulty RNA resulting in a wrong protein being

translated lacking its original activity. This may cause major problems such

as protein aggregation and misfolded proteins, which are not degradable and

result in fatal diseases. Naturally occurring single nucleotide polymorphism

(SNP) among human population may influence gene function and expression

in individuals. Functional variants or genetic changes like SNPs that alter

amino acids in proteins, gene expression, and gene splicing are of great

interest. The first step of regulation is trying to fix problems at the DNA

levels. The next step is to mend at the RNA level through gene splicing and

then at the protein level via proteosome/ubiquitin pathways. In eukaryotes,

higher-level organism, DNA is transcribed to RNA (Pre-mRNA) that

consists of introns and exons. The exons possess the codes that will be

translated into proteins whereas the introns are eventually cut out through

gene splicing. The resulting RNA is referred to as messenger RNA (mRNA).

This messenger RNA may or may not get translated into peptide that folds

into a functional protein.

2. Nucleic Acids: DNA Versus RNA

Nucleic acids are made of long chains of nucletotides that consist of

nitrogenous base, a sugar moiety, and phosphodieseter connections.

Deoxyribonucleic acid (DNA) is basically a sequence of nucleic acids that

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