Contents onlyMolecular Biology
Molecular Biology Support
Scientific Applications Section
AFRC Computing Division
Herts AL5 2JE
Tel:+44 582 762271 Fax: +44 582 761710
This document began, in 1989, as a set of exercises for a training course in
the use of the GCG package. Its intention was to introduce research workers,
including novice computer users, to molecular biology software. The current
document now includes background notes and other software as part of the
training course. The revised aim: to provide a brief introduction to the
facilities available within the AFRC's VAX/VMS network called AGRENET, and
The document was never intended to be a comprehensive coverage of the subject.
Many items of detail are omitted, which were explained during the course. If
the user is prepared to experiment with data and explore on the basis of these
examples, then this document may be of some use. Many users will find
themselves using UNIX-based systems in which case the amendments for using GCG
programs are quite minor: the command line options use a space and a minus
instead of a slash key. eg: on page 3-6 use: mapsort -exclude=388,1020
Summary of contents
Chapter 1 is very AFRC-specific. Chapter 2 is a condensed GCG-reference section
with some AFRC-specific information included. Chapters 3 to 16 contain worked
exercises and background notes. All the examples show how the software behaves
on Agrenet VAXes - some programs default to batch-submission, using local queue
names. All sequences used in the exercises are obtainable from the exercises
themselves, or can be located using Appendix B. Some of the worked examples may
appear different on other VAX systems. A description of the local program
amendments is given in Appendix B.
The course presented was given over a period of two days, although a three day
course might be more appropriate. The order of presentation in the manual is
intended as starting with easier programs, moving to progressively more complex
programs, or where greater explanation is required. A case is easily made for
providing a course with the chapters in a completely different order.
This document is available on the EMBL file server (see Chapter 16.2.1) as
My thanks to the c.500 people who have attended the course for their comments,
criticisms and suggestions for improvements. I am particularly grateful to the
following for their advice and comments.
David Judge - Department of Genetics, University of Cambridge, U.K.
Sarah McQuay - BRU, Kings Buildings, University of Edinburgh, U.K.
Frank Wright - SASS, Kings Buildings, University of Edinburgh, U.K.
The May 1994 version of the document for MS-WORD was prepared at Glaxo
Research & Development, UK; more thanks to Sarah McQuay.
Cary O'Donnell 6th-Sep-1993, 20th May 1994
MOLECULAR BIOLOGY SOFTWARE