Computer Analysis Of Sequence Data Part I

DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gen- ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods ess- tial to analysis, and a familiarity with computers and sequence ana- sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Analysis of Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or p- tein) sequences. Each chapter is written such that a competent sci- tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed pr- tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes enco- tered by users of the sequence analysis software. Software packages for both the mainframe and personal computers are described.

DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gener ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods essen tial to analysis, and a familiarity with computers and sequence analy sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Computer Analysis of Sequence Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or pro tein) sequences. Each chapter is written such that a competent scien tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed prac tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes encoun tered by users of the sequence analysis software.

These comprehensive, up-to-date handbooks are designed for those scientists engaged in the computer analysis of sequence data who want hands-on help in using the most important commercial software available, but simply do not have the time to become computer experts. The expert authors guide you through the programs with easy-to-follow, step-by-step instructions. The topics covered include translations of sequences, sequence alignment, phylogenetic trees, analysis of RNA secondary structure, database searching, submission of data to EMBL/GenBank/DDBJ/etc., maintaining sequence projects, and using patterns to analyze protein sequences. Many chapters have been written by world-class authorities in the field, among them R. Staden, M. Gribskov, D. Higgins, W. Pearson, M. Zuker, and G. Barton. Each volume shares five essential chapters concerning the analysis of sequence data, the FASTA program, converting between sequence formats, obtaining software via INTERNET, and the submission of nucleotide sequence data. Part I covers GCG, MicroGenie, PC/GENE, and FASTA programs. Part II covers Staden and Staden Plus, DNA Strider, FASTA, and MacVector programs.

These comprehensive, up-to-date handbooks are designed for those scientists engaged in the computer analysis of sequence data who want hands-on help in using the most important commercial software available, but simply do not have the time to become computer experts. The expert authors guide you through the programs with easy-to-follow, step-by-step instructions. The topics covered include translations of sequences, sequence alignment, phylogenetic trees, analysis of RNA secondary structure, database searching, submission of data to EMBL/GenBank/DDBJ/etc., maintaining sequence projects, and using patterns to analyze protein sequences. Many chapters have been written by world-class authorities in the field, among them R. Staden, M. Gribskov, D. Higgins, W. Pearson, M. Zuker, and G. Barton. Each volume shares five essential chapters concerning the analysis of sequence data, the FASTA program, converting between sequence formats, obtaining software via INTERNET, and the submission of nucleotide sequence data. Part I covers GCG, MicroGenie, PC/GENE, and FASTA programs. Part II covers Staden and Staden Plus, DNA Strider, FASTA, and MacVector programs.

These comprehensive, up-to-date handbooks are designed for those scientists engaged in the computer analysis of sequence data who want hands-on help in using the most important commercial software available, but simply do not have the time to become computer experts. The expert authors guide you through the programs with easy-to-follow, step-by-step instructions. The topics covered include translations of sequences, sequence alignment, phylogenetic trees, analysis of RNA secondary structure, database searching, submission of data to EMBL/GenBank/DDBJ/etc., maintaining sequence projects, and using patterns to analyze protein sequences. Many chapters have been written by world-class authorities in the field, among them R. Staden, M. Gribskov, D. Higgins, W. Pearson, M. Zuker, and G. Barton. Each volume shares five essential chapters concerning the analysis of sequence data, the FASTA program, converting between sequence formats, obtaining software via INTERNET, and the submission of nucleotide sequence data. Part I covers GCG, MicroGenie, PC/GENE, and FASTA programs. Part II covers Staden and Staden Plus, DNA Strider, FASTA, and MacVector programs.

Computerized sequence analysis is an integral part of biotechnological research, yet many biologists have received no formal training in this important technology. Sequence Analysis Primer offers the beginner the necessary background to enter this vital field and helps more seasoned researchers to fine-tune their approach. It covers basic data manipulation such as homology searches, stem-loop identification, and protein secondary structure prediction, and is compatible with most sequence analysis programs. A detailed example giving steps for characterizing a new gene sequence provides users with hands-on experience when combined with their current software. The book will be invaluable to researchers and students in molecular biology, genetics, biochemistry, microbiology, and biotechnology.

Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.

Understanding sequence data, and the ability to utilize this hidden knowledge, will create a significant impact on many aspects of our society. Examples of sequence data include DNA, protein, customer purchase history, web surfing history, and more. This book provides thorough coverage of the existing results on sequence data mining as well as pattern types and associated pattern mining methods. It offers balanced coverage on data mining and sequence data analysis, allowing readers to access the state-of-the-art results in one place.