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Bioinformatics Sequence and Genome Analysis is written in 10 chapters, which are Historical Introduction and Overview. This chapter provides a brief historical account of the more significant advances that have taken place, as well as an overview of the chapters of this book. Because many contributors cannot be mentioned due to space constraints, additional references to earlier and current reference books, articles, reviews, and journals provide a broader view of the field and are included in the reference lists to this chapter.; Collecting and Storing Sequences in the Laboratory; Alignment of Pairs of Sequences - THIS CHAPTER SUMMARIZES METHODS used to collect sequences of DNA molecules and store them in computer files. Once in the computer, the sequences can be analyzed by a variety of methods. Additionally, assembly of the sequences of large molecules from short sequence fragments can readily be undertaken. Assembled sequences are stored in a computer file along with identifying features, such as DNA source (organism), gene name, and investigator. Sequences and accessory information are then entered into a database. This procedure organizes them so that specific ones can be retrieved by a database query program for subsequent use. Unfortunately, most sequence analysis programs require that the information in a sequence file be stored in a particular format. To use these programs, it is necessary to be aware of these formats and to be able to convert one format to another.; Multiple Sequence Alignment; Prediction of RNA Secondary Structure - starting with this chapter, more detailed discussions of topics, and information on subjects of more peripheral interest, will be available from the Web site for this book. This site is organized according to the same subject headings as this chapter and can be found at http://www.bioinformaticsonline.org. In addition, starting with this chapter, procedural flowcharts will appear at the beginning of the Methods section of most chapters to provide an overview of the methods of analysis. This chapter discusses pair-wise sequence alignment.; Phylogenetic Prediction; Database Searching for Similar Sequences; Gene Prediction; Protein Classification and Structure Prediction; Genome Analysis.