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gcg access wanted

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Mon Jan 24 15:31:35 EST 1994


In <2i12mb$n2k at mserv1.dl.ac.uk> john writes:

> Iwould like some general info on gcg (# and types of different programs
> involved,etc.) as I would like to pursuade our sys admin to have it
> resident on our vax.

Ok then, here you go...


   GCG                                                            (27-SEP-1993)
   === 

   |
   +---Analyse sequences                       
   |   +---Protein Analysis                        
   |   |   +---Search PROSITE Motifs in Proteins       
   |   |   +---Plot a Helical Wheel of a Protein       
   |   |   +---Plot charge as function of pH           
   |   |   +---Plot a PEPTIDESTRUCTURE result          
   |   |   +---Digestion map of a peptide sequence     
   |   |   +---Plot of the helical hydrophobic moment  
   |   |   +---Plot measures of secondary structure    
   |   |   +---Secondary Structure prediction          
   |   |   +---Show fragments of a protein digestion   
   |   |   
   |   +---Comparison                              
   |   |   +---Alignment of the best segments of 2 seqs
   |   |   +---Compare two sequences for similarity    
   |   |   +---Plot COMPARE results                    
   |   |   +---Align two seqs acc. to Needleman/Wunsch 
   |   |   +---Compare two sets of sequences           
   |   |   +---Plot GAP or BESTFIT results             
   |   |   +---Measure percent divergence of 2 proteins
   |   |   
   |   +---Database Searching                      
   |   |   +---Page 2                                  
   |   |   |   +---Create a database library               
   |   |   |   +---Extract sequences from the database     
   |   |   |   +---List sequence names                     
   |   |   |   +---Build hash tables for QUICKSEARCH       
   |   |   |   +---Scan sequence info for a text string    
   |   |   |   +---Print a database sequence on the screen 
   |   |   |   
   |   |   +---Compare sequence to database            
   |   |   +---Find Patterns in database               
   |   |   +---Rapidly indentify a sequence in database
   |   |   +---Align and display WORDSEARCH results    
   |   |   +---Compare peptide seq to nucleic database 
   |   |   +---Display overlaps found by QUICKSEARCH   
   |   |   +---Compare sequence to database            
   |   |   
   |   +---Mapping                                 
   |   |   +---Identify products of T1-nuclease digest 
   |   |   +---Create a restriction map                
   |   |   +---Create a grahpical restriction map      
   |   |   +---Show fragments of a digest by size      
   |   |   
   |   +---Pattern Recognition                     
   |   |   +---Page 2                                  
   |   |   |   +---Create a nucleotide distribution matrix 
   |   |   |   +---Scan a sequence with a CONSENSUS matrix 
   |   |   |   +---Look for similar patterns of codon usage
   |   |   |   +---Look for prokaryotic RNA-pol terminators
   |   |   |   +---Tabulate codon usage                    
   |   |   |   
   |   |   +---Determine nucleotide contents           
   |   |   +---Show open reading frames                
   |   |   +---A frame-specific gene finder            
   |   |   +---Find direct repeats in sequences        
   |   |   +---Plot results of WINDOW                  
   |   |   +---Identify coding seqs without freq.-table
   |   |   +---Make a table of frequencies of patterns 
   |   |   
   |   +---RNA Secondary Structure                 
   |   |   +---Nussinov Plot of RNA secondary structure
   |   |   +---Linear Plot of a folded RNA molecule    
   |   |   +---Find an optimal secondary structure     
   |   |   +---Plot RNA secondary structure from FOLD  
   |   |   +---Plot a MFOLD (Zucker) Result            
   |   |   +---Another plot of a FOLD result           
   |   |   +---Find inverted repeats of RNA sequences  
   |   |   +---Zucker Plot of a RNA Secondary Stucture 
   |   |   
   |   +---Multiple Sequence Analysis              
   |       +---Multiple Sequence Alignment             
   |       +---Find structural motifs in proteins      
   |       +---Make a table of pairwise distances      
   |       +---Optimal alignment between profile & seq 
   |       +---Plot Similarity of Multiple Alignment   
   |       +---Align Multiple Sequences by Yourself    
   |       +---Align and show seqments of similarity   
   |       +---Make a Profile                          
   |       +---Search database with a profile          
   |       +---Display multiple sequences alignment    
   |       
   +---Display                                 
   |   +---Draw a figure or a poster               
   |   +---Create a circular plot of a plasmid     
   |   +---Format sequences for publication        
   |   +---Format and output text                  
   |   +---Simple Text Poster                      
   |   
   +---Gel Fragment Assembly                   
   |   +---Initialize a fragment assembly project  
   |   +---Start the old fragment assembly programs
   |   
   +---Getting Help & Information              
   |   +---Getting Help about GCG                  
   |   +---Introduction to GCG                     
   |   +---Getting Help about GCG-menu             
   |   +---Overview over the GCG menu system       
   |   
   +---Leave the GCG Programs                  
   |   +---Die (some kind of a strange logout)     
   |   +---Go back to DCL (to the dollar prompt)   
   |   +---Leave the System                        
   |   +---Leave the menu environment temporarily  
   |   +---Jump to SQUIRREL (may not be available) 
   |   
   +---Modify sequences                        
   |   +---Editing                                 
   |   |   +---Define keyboard keys for sequence entry 
   |   |   +---Editor for multiple sequence alignment  
   |   |   +---Enter sequence data                     
   |   |   
   |   +---Manipulation                            
   |   |   +---Create new construct out of seq-pieces  
   |   |   +---Insert random mutations into a sequence 
   |   |   +---Simplify sequence into broad categories 
   |   |   +---Extract fragments randomly from seqs.   
   |   |   +---Reverse and/or complement a sequence    
   |   |   +---Randomize the order of a sequence       
   |   |   +---Create a symbol comparison table        
   |   |   
   |   +---Translation                             
   |   |   +---Translate peptide into nucleotide seq   
   |   |   +---Extract a peptide from a MAP result     
   |   |   +---Translate DNA in all six frames         
   |   |   +---Translate nucleotide into peptide seqs  
   |   |   
   |   +---Sequence Exchange                       
   |       +---Exchange from...                        
   |       |   +---From EMBL                               
   |       |   +---From GenBank                            
   |       |   +---From IG                                 
   |       |   +---From PIR                                
   |       |   +---From Staden                             
   |       |   
   |       +---Read a sequence from an other computer  
   |       +---Reformat sequence that it fits to GCG   
   |       +---Send a sequence to a personal computer  
   |       +---Exchange to...                          
   |           +---To FASTA (for e-mail searches at NCBI)  
   |           +---To Fitch (format of Prof. Walter Fitch) 
   |           +---To IG                                   
   |           +---To PIR                                  
   |           +---To Staden                               
   |           
   +---Specials                                
       +---Clear Graphics Display                  
       +---Set Environment for the Current Session 
       |   +---Set Beep                                
       |   |   +---Set Beep On                             
       |   |   +---Set Beep Off                            
       |   |   
       |   +---Switch Command Line Switches            
       |   |   +---Enable Command Line Switches            
       |   |   +---Disable Command Line Switches           
       |   |   
       |   +---Modify Settings for Graphics Output     
       |   |   +---Allow Display of Current Configuration  
       |   |   +---Define Plot Device for Graphics Output  
       |   |   |   +---Laser Printer                           
       |   |   |   |   +---Postscript Laser Printer                
       |   |   |   |   +---Qume QMS Laser Printer                  
       |   |   |   |   
       |   |   |   +---Other                                   
       |   |   |   |   +---XWindow-Driver                          
       |   |   |   |   +---GKS Terminal                            
       |   |   |   |   +---VS-Driver                               
       |   |   |   |   +---VAX Workstation Software                
       |   |   |   |   +---XWindows Terminal                       
       |   |   |   |   
       |   |   |   +---Plotter                                 
       |   |   |   |   +---HP7221 Plotter                          
       |   |   |   |   +---Hewlett-Packard Plotter                 
       |   |   |   |   
       |   |   |   +---REGIS Terminal                          
       |   |   |   +---SIXEL Matrix Printer                    
       |   |   |   +---TEKTRONIX Terminal                      
       |   |   |   
       |   |   +---Inhibit Display of Plot Configuration   
       |   |   +---Select an Available Plot Device         
       |   |   +---View Current Plot Settings              
       |   |   
       |   +---Modify Terminal Printer Port            
       |   |   +---Set Printer Port for Plotting           
       |   |   +---Reset Printer Port from Plotting        
       |   |   
       |   +---Set Sequence Default Format (STADEN/GCG)
       |   +---Tailor Program Documentation            
       |       +---Allow Program Documentation             
       |       +---Disable Program Documentation           
       |       +---Documentation in Output Files           
       |       
       +---File Utilities                          
       |   +---Analyze files                           
       |   |   +---Count the number of characters in a file
       |   |   +---Count characters in a line oriented way 
       |   |   +---Check the identity of two files         
       |   |   +---Read a text file from another computer  
       |   |   +---Print file on a printer of your terminal
       |   |   
       |   +---Send Text Files to Postscriptprinter    
       |   +---Modify files                            
       |       +---Remove blanks and spaces from a file    
       |       +---Replace tab characters with spaces      
       |       +---Convert Long Records to Short Ones      
       |       +---Convert file to all upper/lower case    
       |       +---Replace specific characters of a file   
       |       +---Move file n columns to the left or right
       |       +---Encode/decode a file                    
       |       
       +---Miscellaneous                           
           +---Echo (Shows Keyboard Mapping)           
           +---Plot table of alternate character fonts 
           +---Plot a GKS metafile on a GKS device     
           +---Plot test pattern to check output device
           +---Display Database- and Program-Versions  
           

This was an extract of my GCG-menu ;-)

Regards
   Christoph Gartmann


+----------------------------------------------------------------------------+
| Max-Planck-Institut fuer      Phone   : +49-761-5108-465   Fax: -221       |
| Immunbiologie                 PSI     : PSI%(0262)45050160374::GARTMANN    |
| Postfach 1169                 Internet: gartmann at immunbio.mpg.de           |
| D-79011  Freiburg, FRG                                                     |
+------------- Do you know MENUE, the user environment for VMS? -------------+



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