Computer Analysis of Sequence Data Part II / Edition 1

by Annette M. Griffin, Hugh G. Griffin

Overview

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 analysis 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 protein) 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.

Product Details

ISBN-13:	9780896032767
Publisher:	Springer-Verlag New York, LLC
Publication date:	02/08/1994
Series:	Methods in Molecular Biology , #25
Edition description:	1994
Pages:	433
Product dimensions:	6.10(w) x 9.25(h) x 0.04(d)

About the Author

Griffin, Annette M. (Norwich Research Park); Griffin, Hugh G. (Norwich Research Park)

The contributors represent the specialties of biology, molecular biology, and food research. Most of the contributors come from the U.K., U.S., Germany, Denmark, and Canada. Institutions prominently represented include UCSD, Norwich Research Park-UK, and the European Molecular Biology Laboratory Data Library-Heidelberg.

Table of Contents

Computer Analysis of Sequence Data.- Staden: Introduction.- Staden: Sequence Input, Editing, and Sequence Library Use.- Staden: Managing Sequence Projects.- Staden: Statistical and Structural Analysis of Nucleotide Sequences.- Staden: Searching for Restriction Sites.- Staden: Translating and Listing Nucleic Acid Sequences.- Staden: Searching for Motifs in Nucleic Acid Sequences.- Staden: Using Patterns to Analyze Nucleic Acid Sequences.- Staden: Analyzing Sequences to Find Genes.- Staden: Statistical and Structural Analysis of Protein Sequences.- Staden: Searching for Motifs in Protein Sequences.- Staden: Using Patterns to Analyze Protein Sequences.- Staden: Comparing Sequences.- Staden Plus.- DNA Strider.- MacVector: An Integrated Sequence Analysis Program for the Macintosh.- MacVector: Aligning Sequences.- MacVector: Sequence Comparisons Using a Matrix Method.- MacVector: Restriction Enzyme Analysis.- Mac Vector: Protein Analysis.- Profile Analysis.- Prediction of RNA Secondary Structure by Energy Minimization.- Classification and Function Prediction of Proteins Using Diagnostic Amino Acid Patterns.- Clustal V: Multiple Alignment of DNA and Protein Sequences.- Progressive Multiple Alignment of Protein Sequences and the Construction of Phylogenetic Trees.- The AMPS Package for Multiple Protein Sequence Alignment.- TreeAlign.- Using the FASTA Program to Search Protein and DNA Sequence Databases.- Converting Between Sequence Formats.- Obtaining Software via INTERNET.- Submission of Nucleotide Sequence Data to EMBIVGenBank/DDB J.

Editorial Reviews

Reviewer: James M. Kramer, PhD (Northwestern University Feinberg School of Medicine)
Description: This book describes the use of computer programs contained in three protein/nucleic acid sequence analysis software packages: Staden, DNA Strider, and MacVector. Additionally, use of individual programs for prediction of RNA secondary structure, alignment of sequences, database searching and submission of sequences to the EMBL databank are described.
Purpose: The purpose of this book is to serve as a practical aid for scientists performing computer analyses of protein and/or nucleic acid sequences with these programs. It will help new users learn the programs more quickly and provides useful tips for experienced users.
Audience: The book is targeted at scientists involved in nucleic acid/protein sequence analysis, and who already have basic knowledge of the biology of these molecules. It will be particularly useful for those with little experience using these computer programs, but also contains information that experienced users will appreciate. The multiple authors are all acknowledged experts in the field of computer sequence analysis.
Features: Step-by-step descriptions of how to use the computer programs are provided. Numerous examples of output from the programs are presented as figures. Solutions to some problems commonly encountered with each program are provided at the end of each chapter.
Assessment: This is a very useful book for all researchers involved in computer analysis of protein and/or nucleic acid sequences. It collects in one place basic procedures for use of these computer programs that will aid inexperienced users. The book also provides details of the programs that will be valuable to experienced users.

Doody's Review Service

...a very useful book for all researchers involved in computer analysis of protein and/or nucleic acid sequences. It collects in one place basic procedures for use of these computer programs that will aid inexperienced users...[Also] will be valuable to experienced users.-Doody's Health Sciences Book Review Journal

From the Publisher

3 Stars from Doody

This book describes the use of computer programs contained in three protein/nucleic acid sequence analysis software packages: Staden, DNA Strider, and MacVector. Additionally, use of individual programs for prediction of RNA secondary structure, alignment of sequences, database searching and submission of sequences to the EMBL databank are described. The purpose of this book is to serve as a practical aid for scientists performing computer analyses of protein and/or nucleic acid sequences with these programs. It will help new users learn the programs more quickly and provides useful tips for experienced users. The book is targeted at scientists involved in nucleic acid/protein sequence analysis, and who already have basic knowledge of the biology of these molecules. It will be particularly useful for those with little experience using these computer programs, but also contains information that experienced users will appreciate. The multiple authors are all acknowledged experts in the field of computer sequence analysis. Step-by-step descriptions of how to use the computer programs are provided. Numerous examples of output from the programs are presented as figures. Solutions to some problems commonly encountered with each program are provided at the end of each chapter. This is a very useful book for all researchers involved in computer analysis of protein and/or nucleic acid sequences. It collects in one place basic procedures for use of these computer programs that will aid inexperienced users. The book also provides details of the programs that will be valuable to experienced users.

James M. Kramer

The second of two volumes (see also Part I, 246-9) guiding scientists who may be nonexpert computer users through the most important commercial software programs for the computer analysis of sequence data. Part II treats Staden and Staden Plus, DNA Strider, and MacVector programs. Each volume shares five core chapters concerning the analysis of sequence data, the FASTS program, converting between sequence formats, obtaining software via INTERNET, and the submission of nucleotide sequence data. Plastic comb binding. Annotation c. Book News, Inc., Portland, OR (booknews.com)

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