COURSE (Sequence analysis using the GCG package)

harper at csc.fi harper at csc.fi
Mon Nov 5 05:14:19 EST 1990


The Centre for Scientific Computing in Helsinki Finland, will be holding 
a course on the GCG paqckage from 21-23rd November 1990. The course is free 
to people in Scandinavia, who are attending university, and for people who 
attend universities in the EMBO member countries. The main lecturer will 
be Dr. Reinhard Doelz from the Biozentrum at the University of Basel, 
Switzerland.

Listed below is an outline of the course. Interested people who would 
like to attend should notify HARPER at CSC.FI or BJORKLUND at CSC.FI as soon
as possible.

*********************   PROGRAMME   ***************************
Wednesday 21st November 1990 
 
10:00 -11:00     Introduction. Biosci and EMBL software server  
                 Hardware and software used in Molecular Biology.  
                 Scope and limitations of PCs (IBM+MAC),  
                 Workstations, (Sun, Iris) 
                 Mainframes. (Vax, Unix) 
 
11:00 -11:15     Coffee  
 
11:15 -12:15     VAX Usage  
                 Access (how to log in)  
                 Simple commands:  
                 Viewing, copying, printing, deleting files.  
                 The VAX editor. (EVE, EDT)  
                 Electronic Mail.  
  
12:15 -13:15     Lunch break 
 
13:15 -14:30     Programs available: GCG, PEARSON, NBRF.  
                 Databases available: EMBL, MIPSX, NBRF.  
                 Special databases.  
 
14:30 -14:45     Coffee  
 
14:45 -17:00     Sequences I.  
                 Sequence formats. Sequence format conversion.  
                 The EMBL fileserver. NETSERV at EMBL  
                 How to submit a sequence to the database.  
                 Sequence editing.  
                 Sequence Manipulation, Translation,  
                 Manual Alignment.  
     
18:00            Social get-together at TLP. 
                 Informal meeting with other Finnish molecular        
                 biologists. 
                 Sauna + refreshments.  

Thursday 22nd November 1990 
 
9:00 -10:30      DNA Analysis.  
                 Reading frames,  
                 Statistics,  
                 Restriction maps.  

10:30 -10:45     Coffee 
 
10:45 -12:15     Protein Analysis.  
                 Secondary structure prediction.  
  
12:15 -13:15     Lunch break 
 
13:15 -14:30     Output of results.  
                 Text output of sequences.  
                 Graphics output of GCG graphics.  
                 The GCG program FIGURE  
              
14:30 -14:45     Coffee  
  
14:45 -16:45     Sequence comparison I.   
                 Comparison Matrices  
                 Dotplots.  
                 Alignment path Matrices  
  
16:45 -17:15     Question time  
                 (Ask help with a particular problem) 
  
Friday 23rd November 1990 
 
 
9:00 - 10:30     Sequence comparison II.  
                 Fitting two sequences.  
  
10:30 -10:45     Coffee 
 
10:45 -12:15     Database Searches I.  
                 Algorithm used for fast searches for identity  
                 Algorithm used for searches for homology  
                 FASTEMBL 
                 FAMAIL 
  
12:15 -13:15     Lunch break 
 
13:15 -14:30     Database Searches II.  
                 Digesting the output  
                 Problems and strategies for searching sequences.  
  
14:30 -14:45     Coffee 
 
14:45 -16:45     Database Searches III.  
                 Own databases.  
                 Searching with profiles.  
                 Validation of results.  
                 Significance considerations.  
  
16:45 -17:15     Question time  
                 (Ask help with a particular problem) 
 
Exercise:        Cookbook preparation.  
                 The user gets a if-then-else scheme which can 
                 be worked through on the screen starting from 
                 entering the sequence, doing dna analysis, 
                 translation to protein, protein secondary 
                 structure prediction, database searches, etc.

RGDS -=ROB=-



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