The Internet for Cell and Molecular Biologists
Editors: Andrea Cabibbo1, Richard P. Grant2 and Manuela Helmer-Citterich1
1University of Rome "Tor Vergata", Italy and 2MRC Laboratory of Molecular Biology, Cambridge, UK
Publication date: April, 2002
Pages: c. 368
ISBN: 1-898486-32-8
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This extremely practical guide explains in detail the ever-expanding possibilities that the internet offers cell biologists, molecular biologists, and other bioscientists. All aspects of the internet are discussed from mailing lists and discussion groups to sequence search facilities, primer design software and genome databases. This book is an indispensable manual packed with essential information on the use, purpose and future potential of all relevant resources. A must-have reference book for all bioscience laboratories.
Chapter List
1.
Internet: All You Wanted to Know and Didn't Dare to Ask
Lorenzo M. Catucci and Manuela Helmer-Citterich
1.1 A network of nodes
1.2 Network services
1.3 Short glossary
1.4 References
2.
Select the Right
Computer
Michele Quondam
2.1 CPU
2.2 Memory
2.3 Hard Disk
2.4 Video Card
2.5 Monitors
2.6 Other parts
2.7 The computer power and costs
2.8 A computer to do what?
2.9 Choosing the operating system
3.
Feeling Safe?Think again: Internet
Security
Michele Quondam
3.1 What is a virus
3.2 What is a hacker
3.3 Protection Software
3.3.1 Firewalls
3.3.2 Antivirus Software
3.3.3 Hardware Router with firewall features
3.4 Special e-mail attacks
3.4.1 Bombing
3.4.2 Spamming
3.5 Simple general security rules
4.
Design and Build Your Own Lab/Departmental Home
Page
Andrea Cabibbo
4.1 A global view
4.2 Designing and building the web site
4.2.1 Planning the site with pencil and paper
4.2.2 Building the site
4.2.2.1 Visual html editors
4.2.2.2 Bells and whistles (forms, counters, boards)
4.2.2.3 Short course of HTML: the basics
5.
Using Search Engines Effectively to Find People and
Information
Andrea Cabibbo
5.1 Directories and search engines
5.1.1 Directories
5.1.2 Search engines
5.2 Search syntax: the mathematics of search engines
5.3 Searching for scientific literature: the NCBI PubMed site
6.
Online Tools for Basic Sequence Manipulation, Restriction Analysis, PCR Primers Generation and Evaluation
Andrea Cabibbo
6.1 Restriction analysis
6.2 Basic sequence manipulation
6.3 PCR Primers generation and analysis
6.4 Sequence analysis servers and links
7. Theoretical Aspects of Sequence Alignments
Barbara Brannetti and Allegra Via
7.1 Pairwise alignments
7.1.1 Alignments
7.1.2 Global and local alignment
7.1.3 Substitutions
7.1.4 Insertions and deletions
7.1.5 Statistical significance of alignments
7.2 Multiple alignments
7.2.1 Intoduction
7.2.2 Multiple alignments: why do we need them?
7.2.3 Global and local alignments
7.2.4 Substitutions, deletions and insertions
7.2.5 How do we obtain a multiple alignment?
7.2.6 Gene prediction and pattern matching
7.3 References
8. Analyze a DNA Sequence with Your Browser
Barbara Brannetti
8.1 Genbank database
8.1.1 Description of Genbank database records
8.2 Database search
8.2.1 FASTA
8.2.2 How FASTA works, a step by step description
8.2.3 BLAST
8.3 Gene structure prediction
8.3.1 Filters
8.3.1.1 CENSOR
8.3.1.2 RepeatMasker
8.3.2 Looking for functional sites in DNA sequences
8.3.2.1 Promoter Scan
8.3.2.2 GrailEXP
8.3.2.3 GenScan
8.3.2.4 FGENE
8.3.2.5 GeneMark
8.3.2.6 WebGene
8.3.2.7 GeneId
8.3.2.8 PROCRUSTES
8.4 References
9. Practical Aspects of Protein Sequence Analysis
Allegra Via
9.1 Protein sequence databases
9.1.1 Swissprot-TrEMBL
9.1.2 PIR
9.2 Pair-wise alignments and database searches
9.2.1 FASTA
9.2.2 Fasta3 output
9.2.3 BLAST
9.2.4 BLAST output
9.2.5 Alignment of two sequences
9.2.6 PSI-BLAST
9.2.7 PSI-BLAST output
9.3 Multiple alignments
9.3.1 CLUSTALW
9.3.2 MultAlign
9.3.3 Editing a multiple
alignment
9.3.3.1 ALSCRIPT
9.3.3.2 CINEMA and JALVIEW
9.3.3.3 BOXSHADE
9.4 Hidden Markov Models (HMMs)
9.5 Motifs and patterns
9.5.1 Pattern and domain databases
9.5.1.1 PROSITE
9.5.1.2 BLOCKS
9.5.1.3 PFam
9.5.1.4 PRINTS
9.5.2 Servers for patterns and domains databases scanning
9.5.2.1 ProfileScan
9.5.2.2 BLOCKS server
9.5.2.3 SMART server
9.6 References
10. From Sequence to Structure: an Easy Approach to Protein Structure Prediction
Fabrizio Ferre'
10.1 Principles of protein structure
10.1.1 Introduction
10.1.1.1 Protein structure
10.1.1.2 Techniques for the experimental determination of protein structure
10.1.2 Structures databases
10.1.2.1 The Protein Data Bank and PDBSum
10.1.2.2 SCOP
10.1.2.3 CATH
10.1.2.4 DSSP
10.1.2.5 DALI, FSSP and HSSP
10.1.3 Visualization of molecular structures: molecular graphics tools
10.1.3.1 RasMol
10.1.3.2 SwissPDBViewer
10.1.4 Protein structure comparison
10.2 Protein Structure Prediction
10.2.1 Secondary structure prediction
10.2.1.1 Introduction
10.1.1.2 On the web
10.2.2 Homology Modelling
10.2.2.1 Introduction
10.2.2.2 On the web
10.2.3 Fold Recognition
10.2.3.1 Introduction
10.2.3.2 On the web
10.2.4 Ab initio Prediction
10.2.4.1 Introduction
10.2.4.2 On the web
10.2.5 Evaluation of structure prediction methods
10.3 Transmembrane topology prediction
10.3.1 Introduction
10.3.2 On the web
10.4 Links
10.5 References
11.
Let Others Solve your Problems: the
Newsgroups
Richard P. Grant
11.1 Usenet for beginners
11.2 Bionet
11.3 Access and (n)etiquette
11.4 How to use a news reader
11.5 Whither Bionet?
11.6 Useful links and further reading
12. The Roaming Scientist: Get Online, Manage Your E-mail and Exchange Files from Everywhere
Andrea
Cabibbo
12.1 Getting online
12.1.1 Host institution
12.1.2 Connect from home (Dial-up)
12.1.3 Internet Cafes
12.2 E-mail
12.2.1 How to use your work e-mail account from home or from abroad
12.2.2 Using a web-based e-mail account: read and send e-mail from any computer connected to the internet
12.3 Some tips on file exchange
12.3.1 FTP
12.3.2 Web Site
12.3.3 Web Sharing
13.
Bio-Bookmarks
Andrea Cabibbo and Manuela Helmer-Citterich
13.1 Companies
13.2 Meetings
13.3 Laboratory protocols
13.4 Biological directories and sites
13.5 Microarray resources and databases
13.6 Protein interaction resources
13.7 Useful sites for lessons and presentations
13.8 Biology servers
13.9 Miscellanea
14. Index
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