Training manual available on ftp
odonnell at afrc.ac.uk
odonnell at afrc.ac.uk
Tue Sep 21 03:46:00 EST 1993
Molecular Biology Software Training Manual on ftp
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The AFRC's training manual is available on anonymous ftp from
ftp.embl-heidelberg.de
as the compressed tar file
/pub/doc/afrc_manual.tar.Z
and on the EMBL file server at e-mail address: netserv at embl-heidelberg.de
using the request "get doc:afrc_man.uaa"
Summary
The training manual comprises a contents section, 16 chapters
and four appendices. There are three illustrations: a
front cover and two diagrams for chapter 6 which must be added
separately.
Chapter 1 is very AFRC-specific. Chapter 2 is essentially a
GCG-reference section with some AFRC-specific information included.
Chapters 3-16 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 D.
The separate chapter-files are in postscript form. Each chapter is
formatted for double-sided printing, so some pages are blank.
The contents and preface pages (in plain text) are shown below,
along with a list of the tar file contents.
Dare I say "comments are welcome" ?
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Cary O'Donnell Scientific Support Group, AFRC Computing Division,
West Common, Harpenden, Herts AL5 2JE, United Kingdom
(AFRC = Agricultural & Food Research Council)
Tel: (+44) 582 762271 Internet e-mail: odonnell at afrc.ac.uk
Fax: (+44) 582 761710 Long/Lat 00d 21m 45s West 51d 48m 30s North
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MOLECULAR BIOLOGY SOFTWARE
TRAINING MANUAL
CONTENTS
CHAPTER 1 STARTING SEQUENCE ANALYSIS ON AGRENET
1.1 LOGGING ON . . . . . . . . . . . . . . . . . . . . 1-3
1.2 STARTING UP THE MAIN PACKAGES . . . . . . . . . . 1-3
1.3 USING LOGIN.COM . . . . . . . . . . . . . . . . . 1-4
1.4 OTHER SOFTWARE PACKAGES . . . . . . . . . . . . . 1-4
1.5 HELP INFORMATION . . . . . . . . . . . . . . . . . 1-4
1.6 DOCUMENTATION . . . . . . . . . . . . . . . . . . 1-4
1.7 GRAPHICAL OUTPUT . . . . . . . . . . . . . . . . . 1-4
1.7.1 Unipict files . . . . . . . . . . . . . . . . . 1-5
1.8 SOFTWARE AND DATABASES ON AGRENET . . . . . . . . 1-5
1.9 BROOKHAVEN DATABASE . . . . . . . . . . . . . . . 1-6
1.10 USEFUL VMS COMMANDS . . . . . . . . . . . . . . . 1-6
1.11 QUEUES ON AGRENET . . . . . . . . . . . . . . . . 1-6
1.11.1 Batch queues . . . . . . . . . . . . . . . . . . 1-6
1.11.2 Printer queues . . . . . . . . . . . . . . . . . 1-7
CHAPTER 2 THE GENETICS COMPUTER GROUP PACKAGE
2.1 WHAT IS GCG ? . . . . . . . . . . . . . . . . . . 2-3
2.1.1 Program Examples . . . . . . . . . . . . . . . . 2-3
2.1.2 Command Line Modifiers . . . . . . . . . . . . . 2-3
2.2 DATABASES WITH GCG . . . . . . . . . . . . . . . . 2-4
2.2.1 Database Sequence Names . . . . . . . . . . . . 2-4
2.2.2 Database Accession Numbers . . . . . . . . . . . 2-4
2.2.3 Searching Databases . . . . . . . . . . . . . . 2-4
2.3 DATABASES ON AGRENET . . . . . . . . . . . . . . . 2-5
2.3.1 Nucleic Acid Databases . . . . . . . . . . . . . 2-5
2.3.1.1 Database Divisions . . . . . . . . . . . . . . . 2-5
2.3.2 Protein databases . . . . . . . . . . . . . . . 2-5
2.4 GROUPS OF SEQUENCES . . . . . . . . . . . . . . . 2-6
2.4.1 Files Of Sequence Names . . . . . . . . . . . . 2-6
2.4.2 Multiple Sequence Files . . . . . . . . . . . . 2-6
2.5 PROGRAM DEFAULT VALUES . . . . . . . . . . . . . . 2-6
2.6 GRAPHICS WITH THE GCG PACKAGE . . . . . . . . . . 2-7
2.6.1 Graphics Driver-Selection . . . . . . . . . . . 2-7
2.6.2 Fonts . . . . . . . . . . . . . . . . . . . . . 2-7
2.6.3 GCG 'Figure' Files . . . . . . . . . . . . . . . 2-7
2.7 LOCAL DATA FILES . . . . . . . . . . . . . . . . . 2-8
2.7.1 Enzyme Data Files . . . . . . . . . . . . . . . 2-8
2.8 NUCLEOTIDE SYMBOLS IN GCG . . . . . . . . . . . . 2-9
2.9 AMINO ACID SYMBOLS AND THE STANDARD TRANSLATION
TABLE . . . . . . . . . . . . . . . . . . . . . 2-10
2.10 NUCLEOTIDE SYMBOL COMPARISON TABLE FOR BESTFIT . 2-11
2.11 AMINO ACID SYMBOL COMPARISON TABLE . . . . . . . 2-11
2.11.1 Analysis of symbol comparison values . . . . . 2-12
2.12 PROGRAMS IN THE GCG PACKAGE (RELEASE 7.2) . . . 2-14
2.12.1 Supplementary Programs . . . . . . . . . . . . 2-16
CHAPTER 3 GENERAL SEQUENCE MANIPULATION
3.1 HELP INFORMATION AND DOCUMENTATION . . . . . . . . 3-3
3.1.1 GENHELP - Help on GCG programs. . . . . . . . . 3-3
3.1.2 GENMANUAL - Help by program function . . . . . . 3-3
3.1.3 EASYGCG - Finding your way . . . . . . . . . . . 3-4
3.2 FORMATTING A GCG SEQUENCE . . . . . . . . . . . . 3-4
3.2.1 Formatting raw sequence data . . . . . . . . . . 3-4
3.2.2 DNA <-> RNA conversion . . . . . . . . . . . . . 3-5
3.2.3 Sequence complementing . . . . . . . . . . . . . 3-5
3.3 SEQHELP - HELP FOR OTHER ANALYSIS PROGRAMS . . . . 3-6
3.4 COPYING A DATABASE SEQUENCE . . . . . . . . . . . 3-6
3.5 RESTRICTION MAPPING PROGRAMS . . . . . . . . . . . 3-7
3.5.1 MAP . . . . . . . . . . . . . . . . . . . . . . 3-7
3.5.1.1 Selecting enzymes . . . . . . . . . . . . . . . 3-7
3.5.2 MAPSORT (and selecting enzymes by region) . . . 3-8
3.5.2.1 Digest (and selecting enzymes by name) . . . . . 3-8
3.5.2.2 Creating a plasmid map. . . . . . . . . . . . . 3-9
3.5.3 The enzyme list . . . . . . . . . . . . . . . . 3-9
3.5.4 PROTEIN SEQUENCE MAPPING . . . . . . . . . . . . 3-9
3.5.5 SEQUENCE EDITING . . . . . . . . . . . . . . . 3-10
3.5.5.1 Editing "Modes" . . . . . . . . . . . . . . . 3-10
3.5.5.2 Adding Sequence Data From a File . . . . . . . 3-10
3.5.5.3 Moving Around in the Sequence . . . . . . . . 3-10
3.5.5.4 Editing Comments . . . . . . . . . . . . . . . 3-11
3.5.5.5 Writing Part of the Sequence to a File . . . . 3-11
3.5.5.6 Deleting Part of the Sequence . . . . . . . . 3-11
3.5.5.7 Help . . . . . . . . . . . . . . . . . . . . . 3-11
3.5.5.8 Exiting . . . . . . . . . . . . . . . . . . . 3-11
3.5.5.9 Changing your keyboard . . . . . . . . . . . . 3-11
3.5.6 INTERCONVERTING SEQUENCE FORMATS . . . . . . . 3-12
3.5.6.1 PIR format . . . . . . . . . . . . . . . . . . 3-12
3.5.6.2 STADEN format . . . . . . . . . . . . . . . . 3-12
CHAPTER 4 PROTEIN ANALYSIS
4.1 IDENTIFY OPEN READING FRAMES . . . . . . . . . . . 4-3
4.2 IDENTIFYING POTENTIAL CODING REGIONS . . . . . . . 4-4
4.2.1 Base composition of bulk DNA . . . . . . . . . . 4-4
4.2.2 Base composition in the third codon position . . 4-5
4.2.3 Codon usage bias . . . . . . . . . . . . . . . . 4-5
4.3 TRANSLATING RNA INTO PROTEIN . . . . . . . . . . . 4-6
4.3.1 Three and one-letter abbreviations . . . . . . . 4-6
4.4 PREDICTING SECONDARY STRUCTURE IN PROTEINS . . . . 4-7
4.4.1 PEPTIDESTRUCTURE & PLOTSTRUCTURE . . . . . . . . 4-7
4.4.2 MOMENT . . . . . . . . . . . . . . . . . . . . . 4-8
4.4.3 PEPPLOT . . . . . . . . . . . . . . . . . . . . 4-8
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