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

    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" ?

 *************************************************************************
 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
 -------------------------------------------------------------------------


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


                            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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