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HGMP-RC 2-day course on GCG

Gary Williams x3294 gwilliam at mrc-crc.ac.uk
Mon Oct 4 08:25:53 EST 1993


			2-day GCG course
			----------------

The UK MRC's HGMP-RC will be running a 2-day course on the GCG
(Wisconsin) package at Harrow on the 7th and 8th of February 1984. 

The main objective is to introduce and familiarise users with the GCG
sequence analysis package.  This is one of our most frequently used and
useful packages.  It consists of a large number of programs covering
most areas of sequence analysis. 

A little knowledge in the use of computers will be desirable.  No
previous experience of GCG will be assumed, but would be beneficial. 
The course will involve lots of practical exercises to illustrate the
use of the package.  A few non-GCG programs will be introduced, where
they have advantages over GCG programs. 

Provisional course structure:

Day 1)
	Brief Introduction to running GCG under Unix:
		Text files
		Directories

	GCG's Databases:
		The databases available.
		Accessing sub-sections of the database.
		Formats of common databases (Accession number etc.)

	Typical GCG programs:
		Obtaining sequences (fetch, typedata)
		Translating sequences (translate)
		Keyword searches (stringsearch)

	Obtaining help:
		genhelp
		genman

	Sequence Entry:
		GCG sequence formats
		Conversion programs (fromstaden, topir)
		Entering a sequence (seqed)
		Reformating a file (reformat)

	Applications:
		Graphics output (X-Windows, Postscript, HPGL, Tektronix)
		Restriction mapping (map, mapplot)
		Alignment (gap/bestfit)
		Sequence comparison (compare, dotplot)

	Batch processing in GCG:
		(stringsearch)

Day 2) 
	Creating own Databases:
		Use of files of filenames (stringsearch)		
		Mini-databases (dataset)

	Multiple Alignment:
         	Multiple alignment (pileup)
		Editing muliple alignments (lineup)
		Printing multiple alignment (non-GCG program: alscript)

	Database Searching:
		Searching with non-GCG programs (Edinburgh DAP, blast, fasta)
         	Searching for patterns (findpattern)
 		Searching for protein motifs (motif)

	Other useful applications:
		RNA folding (foldrna, mfold, plotfold)
		Protein secondary structure prediction, (peptidestructure)

	Own Work:
		Have a task you would like to use GCG for.
		Work through it and ask lots of questions.

	Future Direction of GCG:
		Quick talk about this and the implications,
                  such as the next release of GCG.
                Perhaps talk about complementary packages, eg. Staden


The course will be free to HGMP-RC registered users.  There is a fee of
400 Pounds for non-registered or commercial users. 

To book, contact:

	Mrs. Christine Bates
	HGMP Resource Centre,
	Clinical Resource Centre
	Watford Road,
	HARROW, HA1 3UJ, UK

	Tel: (+44) 81 869 3446
	Fax: (+44) 81 869 3807
	Email: c.bates at hgmp.mrc.ac.uk
-- 
GARY WILLIAMS,  Computing Services,       Janet:     G.Williams at UK.AC.MRC.HGMP
MRC Human Genome Mapping Project,         Internet:  G.Williams at HGMP.MRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK      ** Sequence databases have  **
Tel 081-869 3294   Fax 081-423 1275         ** about a 3% error content **



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