Computer Analysis of Sequence Data Part II / Edition 1

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Overview

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.

The book contains black-and-white illustrations.

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Editorial Reviews

Doody's Review Service
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.
James M. Kramer
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.
Booknews
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)

3 Stars from Doody
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Product Details

  • ISBN-13: 9780896032767
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 2/8/1994
  • Series: Methods in Molecular Biology Series , #25
  • Edition description: 1994
  • Edition number: 1
  • Pages: 445
  • Product dimensions: 9.00 (w) x 6.00 (h) x 1.00 (d)

Table of Contents

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: A Macintosh Program for Handling Protein and Nucleic Acid Sequences. MacVector: An Integrated Sequence Analysis Program for the Macintosh. MacVector: Aligning Sequences. MacVector: Sequence Comparisons Using a Matrix Method. MacVector: Restriction Enzyme Analysis. MacVector: 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 EMBL/GenBank/DDBJ. Index.

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