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:
Brief Introduction to running GCG under Unix:
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)
GCG sequence formats
Conversion programs (fromstaden, topir)
Entering a sequence (seqed)
Reformating a file (reformat)
Graphics output (X-Windows, Postscript, HPGL, Tektronix)
Restriction mapping (map, mapplot)
Sequence comparison (compare, dotplot)
Batch processing in GCG:
Creating own Databases:
Use of files of filenames (stringsearch)
Multiple alignment (pileup)
Editing muliple alignments (lineup)
Printing multiple alignment (non-GCG program: alscript)
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)
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
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 **