This 'Survival' Guide is intended to serve as a cookbook for the casual
user of computers in molecular biology. It is not intended to explain
science or make the programs' algorithms more transparent. The Biocomputing
Tutorial (Doelz, R. 1990) included more background informantion, and
worked-out examples available.
The Guide focuses mostly on the GCG software; (Genetics Computer Group,
(1991), Program Manual for the GCG Package, Version 7, April 1991, 575
Science Drive, Madison, Wisconsin, USA 53711), but also includes examples
from the ATLAS software from PIR International and the SRS software from
T.Etzold, EMBL.
This is the first version of the Biocomputing Survival Guide. It will be
updated according to demand. If there are changes and additions,
incremental versions will be available electronically, and major releases
will be printed.
Version 1.1
A couple of minor spelling and typographic additions and changes.
Version 1.1 is now also available as MS-DOS self-extracting MS Word
document.
***NEW***
This book can be purchased in Switzerland from Reinhard Doelz, Biocomputing,
Biozentrum der Universtiaet, Klingelbergstrasse 70, CH 4056 Basel, Switzerland.
International Inquiries please to Paula Maki-Valkkila, CSC, Tietotie 6, P.O.Box
405, 02101 Espoo, Finland. It can also be obtained via anonymous ftp from
bioftp.unibas.ch mirror nic.switch.ch [130.59.1.40].
Regards
Reinhard
Survival_Guide_1.hqx -----> binhexed from Mac (APPLE only,ASCII)
surgid_1.exe ------------> self-extracting binary (DOS only)
+----------------------------------+-------------------------------------+
| Dr. Reinhard Doelz | RFC doelz at urz.unibas.ch |
| Biocomputing | DECNET 20579::48130::doelz |
|Biozentrum der Universitaet | X25 022846211142036::doelz |
| Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078
| CH 4056 Basel | TEL x41 61 267- 2076 or 2247 |
+------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+
ftp mirror at nic.switch.ch
-----------------------------------------
List of contents follows.
-------------------------
BIOCOMPUTING SURVIVAL GUIDE, (C) R.Doelz, 1993
0. Preface 2
0.1. Intended Audience 2
0.2. Copyright 2
0.3 Acknowledgements 2
0.4. Availability of the Survival Guide 2
1. COMPUTERS
Basics 3
1.1. Your Requirements 3
1.2. In order to connect... 3
1.3. Once you have made the connection ... 6
1.4.If you successfully logged in 7
1.5.If you need to change your password 8
1.6. Disconnect 9
EMERGENCY BREAK 10
2. COMPUTERS
Common Problems 11
2.1. No response (screen stays dark) 11
2.2. No response (after screen worked) 11
2.3. No connection to host 11
2.4. No successful login 12
2.5. During Session 13
2.6. No response any more (but worked earlier) 14
2.7. Keys give wrong response 15
2.8. Need to delete lock file 15
2.9. Quota exceeded 15
2.10. Need to stop a previous session 16
3. COMPUTERS
File handling 18
3.1. Command overview 18
3.2. File editing on VMS 19
3.3. File editing on UNIX 19
4. BIOLOGY
Setup of Environment 21
4.1. Calling the GCG Setup Program 21
4.2 Setup of GCG Plotting environment 21
4.3 Using X-Windows Across the Network
4.4 Verification of the plotting environment 22
5. BIOLOGY
Entering a Sequence 23
5.1 Enter your Sequence (from scratch) 23
5.2. Sequence Modification 23
5.3. Import Sequence From Other Sources 24
5.4. VMS import from other VMS hosts via DECNET 27
5.5. UNIX import from other UNIX hosts via remote copy 27
5.6. Reformatting from RNA, DNA, MSF or other 28
5.7. Reformatting from other sequence formats 28
6. BIOLOGY
Get sequence from the database 29
6.1. From Local Database 29
6.2. View sequence data 31
6.3. Using Electronic mail to get Sequences 33
6.4. Using GOPHER get Sequences 35
7. HELP
Computer and Biology 36
7.1. Computer on-line documentation 36
7.2. GCG on-line documentation 36
7.3. ATLAS on-line documentation 37
7.4. SRS on-line documentation 37
7.5. GOPHER, KERMIT, FTP etc on-line documentation 37
7.6. Network help 37
7.7. Printed documentation 39
8.BIOLOGY
Handle a single sequence 40
8.1. Composition 40
8.2. DNA Reading frame display 40
8.3. DNA Restriction enzyme mapping 41
8.4. Translation 43
8.5 Protein Tools 44
9. BIOLOGY
Comparison of two sequences 45
9.1. Graphical representation 45
9.2. Comparison of two sequences of similar length 46
9.3. Comparison of two sequences of different length 46
9.4. Graphical display of two aligned sequences 46
9.5. Significance evaluation 47
10. BIOLOGY
One sequence against many. 48
10.1. Tools for sequence searching 48
10.2. Searching Strategies 49
10.3. Use of Searching Libraries 50
11. BIOLOGY
Using sequences simultaneously 52
11.1. How to get more than one sequence 52
11.2. Processing Automatic Sequence Alignments 54
11.3 Processing Manual Sequence Alignments 57
12. BIOLOGY
The world of patterns 58
12.1 DNA pattern searching 58
12.2. Protein pattern searching 59
12.3 Searching with a profile 60
