数据库

With genome-wide gene expression microarrays being increasingly applied in various areas of biomedical research, the diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this chapter, we describe a generalized fr ...

The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing ...

In this chapter, we demonstrate the usability of the KEGG (Kyoto encyclopedia of genes and genomes) databases and tools, especially focusing on the visualization of the omics data. The desktop application KegArray and many Web-based tools are tightly integrated with the KEGG knowledgeb ...

DNA microarray technology has been used for genome-wide gene expression studies that incorporate molecular genetics and computer science analyses on massive levels. The availability of microarrays permit the simultaneous analysis of tens of thousands of genes for the purposes of g ...

This chapter surveys the use of fixed-parameter algorithms in phylogenetics. A central computational problem in this field is the construction of a likely phylogeny (genealogical tree) for a set of species based on observed differences in the phenotype, differences in the genotype, or gi ...

The historical movement of organisms, whether recent or in the distant past, forms a central aspect of evolutionary studies. Inferring patterns of migration can be difficult and requires reliance on a large suite of bioinformatic tools. As it is primarily the movement of groups of related indi ...

Recombination is the major motor of evolution. While mutations result in gradual changes, recombination reshuffles entire functional modules and thus progresses evolution in leaps and bounds. We need to identify recombination breakpoints in sequences to understand the evolut ...

Nucleotide sequences of microbial genomes provide evidence that genes have been shared among organisms, a phenomenon known as lateral genetic transfer (LGT). Hypotheses about the importance of LGT in the evolution and diversification of microbes can be tested by analyzing the extens ...

The chromosomes of mammalian genomes exhibit reasonably high levels of similarity that can be used to study small-scale sequence variations. A different approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene or segment orders. This ...

With the recent sequencing of numerous complete genomes and the advent of high throughput technologies (e.g., yeast two-hybrid assays or tandem-affinity purification experiments), it is now possible to estimate the ancestral form of protein interaction networks. This chapter comb ...

The Double Cut and Join is an operation acting locally at four chromosomal positions without regard to chromosomal context. This chapter discusses its application and the resulting menu of operations for genomes consisting of arbitrary numbers of circular chromosomes, as well as for a gen ...

To explain the evolutionary mechanisms by which populations of organisms change over time, it is necessary to first understand the pathways by which genomes have changed over time. Understanding genome evolution requires comparing modern genomes with ancestral genomes, which thus ...

Most phylogenetic methods are model-based and depend on Markov models designed to approximate the evolutionary rates between nucleotides or amino acids. When Markov models are selected for analysis of alignments of these characters, it is assumed that they are close approximations of ...

Methods to detect the action of selection on proteins can now make strong predictions about its strength and location, but are becoming increasingly technical. The complexity of the methods makes it difficult to determine and interpret the significance of any selection detected. With mo ...

Molecular phylogenetics examines how biological sequences evolve and the historical relationships between them. An important aspect of many such studies is the estimation of a phylogenetic tree, which explicitly describes evolutionary relationships between the sequence ...

DNA and amino acid sequences contain information about both the phylogenetic relationships among species and the evolutionary processes that caused the sequences to divergence. Mathematical and statistical methods try to detect this information to determine how and why DNA and pr ...

In recent years, genome-wide detection of alternative splicing based on Expressed Sequence Tag (EST) sequence alignments with mRNA and genomic sequences has dramatically expanded our understanding of the role of alternative splicing in functional regulation. This chapter revi ...

Gene-finding is concerned with the identification of stretches of DNA in a genomic sequence that encode biologically active products, such as proteins or functional non-coding RNAs. This is usually the first step in the analysis of any novel piece of genomic sequence, which makes it a very impor ...

Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. S ...

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