HELP!

On-Line

World Wide Web
at the UNIX prompt>
Frequently Asked Questions
Usenet News Groups

Manuals

Node-specific User Support

Extra exercises (for the very keen)

On-Line Help

• World Wide Web
  • Staden pages
  • GCG web site
  • EGCG documentation

• at the UNIX prompt>
  • genhelp programmename - GCG help ordered by programme name
    - Lists all GCG programmes.
    - Help information arranged hierarchically.
    - Subtopics describe a programme's function and details of its input and output.
    - Very useful for discovering how to change a programme's performance.
    - "? <RETURN>" lists the subtopics.
    

    - Generally useful subtopics are:

    "example", which displays an example use of the programme.

    "command-line", which shows you the command line switches so you may change the programme's default settings.

    "local_data_files", which shows you the data files the program uses or could use.

    - "<RETURN>" takes you back to the previous layer.
    

  • genman - GCG help organised by programme function
    - Same information as with genhelp.
    - Programmes are grouped by function.
    - Useful in identifying the required programme(s).

  • egenhelp programmename - EGCG help ordered by programme name

  • egenman - EGCG help organised by programme function

• Frequently Asked Questions
  • Staden FAQ - from Tim Littlejohn
  • GCG FAQ - newsgroup version
                      - WWW version from GCG (coming soon!)
                      - WWW version from HGMP (*** wrong URL! ***)

• Usenet News Groups
  • bionet.software.staden
  • bionet.software.gcg

Node-specific User Support

	EMBnet Node	UNIX command(s)	Menu Command(s)	Person/EMail	Telephone/FAX
	BioBase	menu, data, pgms, auxi	?	Hans Ullitz-Moeller	+45 89 12 28 46
				Bo Mikkelsen	+45 89 12 ?? ??
	HGMP		??; ??;??	User Support	+44 1223 494 520
			faq		+44 1223 494 512

Extra Exercises

Exercise DNA Analysis - HELP! 1: use genhelp

List all the available GCG programmes for which on-line help is available. Look at the help documentation for map.

prompt> genhelp

GenHelp

To get help with the Wisconsin Package, type the first few letters of any of the topics in the index list. The GCG command % genmanual (as opposed to % genhelp) will give you help that is organized like the Wisconsin Package Program Manual. Additional information available: 8.0_What's_New 8.1_What's_New Appendix_III Appendix_VI ASSEMBLE BACKTRANSLATE BESTFIT BLAST CHOPUP CIRCLES CODONFREQUENCY CODONPREFERENCE COMPARE COMPOSITION COMPRESSTEXT COMPTABLE CONSENSUS CORRESPOND CORRUPT COUNT CRYPT Database_Tables DATASET DBINDEX ... Topic? map MAP Map displays both strands of a DNA sequence with restriction sites shown above the sequence and possible protein translations shown below. Additional information available: DESCRIPTION EXAMPLE OUTPUT RELATED_PROGRAMS RESTRICTIONS SUBSET,_OVERLAP,_AND_PERFECT_SEARCHES DISPLAY_CONVENTIONS SELECTING_ENZYMES CHOOSING_THE_TRANSLATION_FRAMES OPEN_READING_FRAMES POTENTIAL_RESTRICTION_SITES SEARCH_FOR_ANY_SEQUENCE_PATTERN DEFINING_PATTERNS PRIMER_WALKING SEQUENCE_TYPE COMMAND-LINE_SUMMARY ACKNOWLEDGEMENT LOCAL_DATA_FILES OPTIONAL_PARAMETERS MAP Subtopic?

Look at three of these subtopics. You can use the unique abbreviations of the subtopic names to save typing, e.g., com for command-line_summary.

Suggestions for other extra exercises are welcomed!