User's Guide for GCG ?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Mon Jun 21 10:05:13 EST 1993


In article <930621.083953.6013 at medinfo.rochester.edu>, charles at MEDINFO.ROCHESTER.EDU ("Charles A. Alexander") writes:
|> >Earlier this year I recall a series of messages about a Users Guide to GCG
|> >being produced by someone on the list. I have lost track of those messages.
|> >Did this document get produced?
|> >
|> That person was me.  We have been busy with the installation of a new VMS system 
|> here for biocomputing and the user guide revision has been on the backburner.  
|> But I have begun to pick at it and will probably have it ready in a month.
|> My apologies to all the other netters who expressed an interest.  I have not 
|> forgotten who you are and will post to bio-soft as soon as it is done.
|> 

On our ftp server there is a (preliminary) version of the 
'biocomputing survival guide' in the archive_data/survival 
subdirectory. It is a Mac MS WORD hqx file. We anticipate 
to print a slightly refined version in the very near future. 
The document index is appended below. It focuses on software 
which is typically installed at a site which runs GCG software, 
and covers both VMS and UNIX. 

Regards
Reinhard 

============================================================================






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


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