MTU Cork Library Catalogue

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Bioinformatics : a biologist's guide to biocomputing and the Internet / Stuart M. Brown.

By: Brown, Stuart M, 1962-.
Material type: materialTypeLabelBookPublisher: Natick, MA : Eaton, c2000Description: xi, 188 p. : ill. ; 25 cm. + hbk.ISBN: 188129918X.Subject(s): Bioinformatics | Molecular biology -- Data processingDDC classification: 570.285
Contents:
Section I An overview of bioinformatics: Introduction -- Genomics and the genome project -- The role of computers in the biology laboratory -- Section II Computer tools for sequence analysis: Finding and retrieving sequences in databases -- Similarity searching -- Pairwise and multiple alignment -- Structure-function relationships -- Plasmid mapping and PCR primer design -- DNA sequencing -- Phylogenetics.
Holdings
Item type Current library Call number Copy number Status Date due Barcode Item holds
General Lending MTU Bishopstown Library Lending 570.285 (Browse shelf(Opens below)) 1 Available 00082907
General Lending MTU Bishopstown Library Lending 570.285 (Browse shelf(Opens below)) 1 Available 00082908
Total holds: 0

Enhanced descriptions from Syndetics:

For biologists, students, or interested amateurs, Brown (cell biology, New York U.) provides an overview to help researchers evaluate and choose the appropriate software, databases, and Web sites for various analysis tasks, and to select options within various software packages. He describes programs for mainframes and personal computers, and those freely available on the Web. The disk contains several software packages. Annotation c. Book News, Inc., Portland, OR (booknews.com)

Includes bibliographical references and index.

Section I An overview of bioinformatics: Introduction -- Genomics and the genome project -- The role of computers in the biology laboratory -- Section II Computer tools for sequence analysis: Finding and retrieving sequences in databases -- Similarity searching -- Pairwise and multiple alignment -- Structure-function relationships -- Plasmid mapping and PCR primer design -- DNA sequencing -- Phylogenetics.

Table of contents provided by Syndetics

  • Section I An Overview of Bioinformatics
  • 1 Introduction (p. 3)
  • A Bioinformatics Survival Guide (p. 3)
  • The Integration of Software, Databases, and the Web (p. 5)
  • Integrated Databases (p. 8)
  • 2 Genomics and the Genome Project (p. 11)
  • Genomics (p. 11)
  • Genome Sequencing (p. 11)
  • Raw Genome Sequence Data (p. 14)
  • Expressed Sequence Tags (p. 14)
  • Polymorphisms (p. 15)
  • DNA Chips (p. 16)
  • Comparative Genomics (p. 17)
  • Genome Bioinformatics (p. 19)
  • The Genome Annotation Problem (p. 20)
  • The Genome Project and the Internet (p. 22)
  • Genomics and Pharmaceutical Research (p. 24)
  • 3 The Role of Computers in the Biology Laboratory (p. 27)
  • Computers in the Laboratory (p. 27)
  • A Brief History of the Internet (p. 30)
  • Using Computers for Biology Research (p. 33)
  • Types of Computers (p. 34)
  • Network Computers (p. 35)
  • Working with Mainframes, Personal Computers, and the Web (p. 37)
  • Why GCG? (p. 38)
  • Section II Computer Tools For Sequence Analysis
  • 4 Finding and Retrieving Sequences in Databases (p. 47)
  • Public Databases (p. 47)
  • Entrez (p. 48)
  • Sequence Retrieval System (p. 55)
  • Genetics Computer Group Lookup and Fetch (p. 56)
  • 5 Similarity Searching (p. 57)
  • Introduction to Sequence Similarity (p. 57)
  • Dot Plots (p. 60)
  • Distances (p. 61)
  • Similarity Searches on the World Wide Web (p. 64)
  • Databases (p. 65)
  • Fasta (p. 68)
  • FASTA Format (p. 69)
  • BLAST (p. 72)
  • BLAST Considerations (p. 76)
  • BLAST versus FASTA (p. 77)
  • General Tips for Similarity Searching (p. 78)
  • Other Similarity Search Methods (p. 80)
  • Interpretation of Output (p. 82)
  • 6 Pairwise and Multiple Alignment (p. 85)
  • Introduction to Alignment (p. 85)
  • Global versus Local Alignments (p. 87)
  • Multiple Sequence Alignment (p. 89)
  • Editing and Formatting Multiple Alignments (p. 96)
  • 7 Structure-Function Relationships (p. 99)
  • Protein Structure and Function (p. 99)
  • Finding Genes in DNA Sequences (p. 100)
  • DNA Signal Sequences (p. 102)
  • RNA Structure (p. 103)
  • Protein Structure (p. 104)
  • Protein Composition and Secondary Structure (p. 108)
  • Protein Tertiary Structure (p. 112)
  • Motifs (p. 113)
  • Profiles (p. 114)
  • Searching for New Motifs (p. 116)
  • 8 Plasmid Mapping and PCR Primer Design (p. 121)
  • Restriction Mapping (p. 121)
  • DNA Strider (p. 123)
  • MacVector and OMIGA (p. 125)
  • Gene Construction Kit (p. 126)
  • Vector NTI (p. 127)
  • Primer Design for PCR and Sequencing (p. 129)
  • Primer Design Programs (p. 129)
  • 9 DNA Sequencing (p. 133)
  • The Biochemistry of DNA Sequencing (p. 133)
  • Sequencing Strategies (p. 135)
  • Software Recommendations (p. 140)
  • 10 Phylogenetics (p. 145)
  • Taxonomy and Phylogenetics (p. 145)
  • Some Caveats (p. 149)
  • Cladistic versus Phenetic Analysis Methods (p. 150)
  • Calculating Distances (p. 151)
  • Clustering Algorithms (p. 152)
  • Cladistic Methods: Parsimony (p. 153)
  • Cladistic Methods: Maximum Likelihood (p. 155)
  • Computer Software (p. 155)
  • GCG (p. 156)
  • PAUP (p. 156)
  • PHYLIP (p. 156)
  • MacClade (p. 158)
  • Phylogenetics on the Web (p. 158)
  • Conclusions (p. 159)
  • Section III Appendices
  • Glossary (p. 163)
  • Bioinformatics Software (p. 175)
  • Index (p. 181)

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