Printed version of the Biocomputing Survival Guide available

Reinhard Doelz doelz at comp.bioz.unibas.ch
Fri Aug 13 08:59:10 EST 1993


[Note from the moderator, D.K. - I have been assured that the price of
this guide below is intended only to cover costs of the hardcopy
version.]

If you ever had trouble to spell out the basic file handling 
commands correctly, or forgot how to ftp a file from a VMS archive
if you are on UNIX, or if you find the extensive GCG documentation 
too difficult to read, then the Biocomputing Survival Guide is 
for you. On 60 pages you will learn on the most important 
commands of either UNIX or VMS systems and the GCG software. 
ATLAS and SRS are mentioned also. 

This book is not intended to be the scientific explanation of the 
software, it is thought as 1st aid. 
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 as printed booklet. 
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 

-- 
+----------------------------------+-------------------------------------+
|    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 
               -----------------------------------------
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



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