生物信息学技术

The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domai ...

This chapter gives an overview of the most commonly used biological databases of nucleic acid sequences and their structures. We cover general sequence databases, databases for specific DNA features, noncoding RNA sequences, and RNA secondary and tertiary structures.

Proteins are composed of functional units, or domains, that can be found alone or in combination with other domains. Analysis of protein domain architectures and the movement of protein domains within and across different genomes provide clues about the evolution of protein function. The c ...

Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic d ...

Protein sequence databases do not contain just the sequence of the protein itself but also annotation that reflects our knowledge of its function and contributing residues. In this chapter, we will discuss various public protein sequence databases, with a focus on those that are generally a ...

Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a key role in the regulation of metabolic steps within the cells, as drug targets, and in a wide range of biotechnological applications. With respect to reaction type, they are grouped into six classes, name ...

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. Th ...

From the database point of view, biomolecular pathways are sets of proteins and other biomacromolecules that represent spatio-temporally organized cascades of interactions with the involvement of low-molecular compounds and are responsible for achieving specific phenot ...

In the current understanding, translation of genomic sequences into proteins is the most important path for realization of genome information. In exercising their intended function, proteins work together through various forms of direct (physical) or indirect interaction mech ...

Neural networks are a class of intelligent learning machines establishing the relationships between descriptors of real-world objects. As optimisation tools they are also a class of computational algorithms implemented using statistical/numerical techniques for param ...

Cluster analysis is an unsupervised pattern recognition frequently used in biology, where large amounts of data must often be classified. Hierarchical agglomerative approaches, the most commonly used techniques in biology, are described in this chapter. Particular attention is ...

The present chapter provides the basic information about the measures of proximity between two subjects or groups of subjects. It is obvious that these concepts must be clear in order to apply them to any pattern recognition analysis, both supervised and unsupervised.

The Support Vector Machine (SVM) is a widely used classifier in bioinformatics. Obtaining the best results with SVMs requires an understanding of their workings and the various ways a user can influence their accuracy. We provide the user with a basic understanding of the theory behind SVMs and f ...

Given the amount of sequence data available today, in silico function prediction, which often includes detecting distant evolutionary relationships, requires sophisticated bioinformatic workflows. The algorithms behind these workflows exhibit complex data structur ...

Markov and Hidden Markov models (HMMs) are introduced using examples from linkage mapping and sequence analysis. In the course, the forward–backward, the Viterbi, the Baum-Welch (EM) algorithm, and a Metropolis sampling scheme are presented.

High-throughput DNA sequencing is increasing the amount of public complete genomes even though a precise gene catalogue for each organism is not yet available. In this context, computational gene finders play a key role in producing a first and cost-effective annotation. Nowadays a compi ...

Noncoding RNAs (ncRNAs) are increasingly recognized as important functional molecules in the cell. Here we give a short overview of fundamental computational techniques to analyze ncRNAs that can help us better understand their function. Topics covered include prediction of seco ...

In recent years it was shown that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins are ubiquitary proteins that fulfill essential biological functions while lacking a stable 3D structure. Despite the large abundance of disorder, ...

If posttranslational modifications (PTMs) are chemical alterations of the protein primary structure during the protein’s life cycle as a result of an enzymatic reaction, then the motif in the substrate protein sequence that is recognized by the enzyme can serve as basis for predictor cons ...

The quaternary structure (QS) of a protein is determined by measuring its molecular weight in solution. The data have to be extracted from the literature, and they may be missing even for proteins that have a crystal structure reported in the Protein Data Bank (PDB). The PDB and other databases derived ...