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? -------------+
