Contents onlyMolecular Biology Software

Training Manual

Molecular Biology Support

Scientific Applications Section

AFRC Computing Division


Herts AL5 2JE



Tel:+44 582 762271 Fax: +44 582 761710

May 1994



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 beyond.

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 -six/

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

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 MS-WORD files.


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