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GCG Menu

tekaia at pasteur.fr tekaia at pasteur.fr
Fri Oct 29 05:32:34 EST 1993


In article <9310281935.AA27964 at ugene1.abbott.com> bollingt at ugene1.abbott.com (Tim Bolling) writes:
>Robert DeLisio writes...
>
>>From BIOSCI-REQUEST at net.bio.net Wed Oct 27 15:09:15 1993
>>Date: Wed, 27 Oct 93 16:05:13 EDT
>>From: Bob DeLisio <delisior at rnisd0.DNET.roche.com>
>>To: info-gcg at net.bio.net
>>Subject: GCG Menu
>>Content-Length: 853
>

>Beng-Kee Kiong and Tin-Wee Tan described (in CABIOS 9(2):211-214, 1993) 
>a UNIX menuing system which they developed for the GCG programs based on a 
>hypertext-like navigation program called HYTELNET (Scott and Fogel, 1991).
[...]
I fully agree with the comments of Tim Bolling, and also would like to thank
Tin-Wee and Ben-Kee for their usefull and easy to use programs.
Their latest reference is :
A general UNIX interface for biocomputing and network information retrieval
software B.K.Kiong and T.W.Tan  CABIOS 9(5) p.581-86 1993.

I used their programs to construct our local SIS_MENU on SUN and CONVEX
servers. Here is an overview of its GCG related part. This might be of 
interest for UNIX users and give an idea of how it looks like.
Sorry if it is too long.
Fredj Tekaia
----------------------------------------------------------------------------
Fredj Tekaia				Service d`Informatique Scientifique
tekaia at pasteur.fr			Institut Pasteur
					25, rue du Dr. Roux
					75724 Paris cedex 15	France
----------------------------------------------------------------------------
 
bash$ SIS_MENU

	Service d'Informatique Scientifique - Institut Pasteur

--->	[SAS]		Sequence Analysis Software
	[DB]		Search Databases, Entrez and Biogophers
	[INT]		Internet resources
	[LINKAGE]	Linkage Analysis Programs
	[seminaires]	Seminaires
	[HELP]		INDEX of Help files

		Read the Copyright [COPYRIGHT]
?)help q)quit !)unix, arrow keys to navigate/select, [directory browser]
---------------------------------------------------------------------------
	SEQUENCE ANALYSIS SOFTWARE

---->	[GCG]	GCG sequence analysis package
	[STA]	STADEN package
	[BLAST] Basic Local Alignment Search Tool programs
	[BLKSRCH]	Blocks homology Search
	[GETBLOCK]	Get a block and related PROSITE informations
	[PLS]	PLSEARCH sensitive protein-family database search
	[PRO]	PROSEARCH protein sequence motifs search on PROSITE db
	[RE]	READSEQ sequence format interconversion
	[SAPS]	Statistical Analysis of Protein Sequences
	[PIMA]	Pattern-induced multisequence alignment program
	[CLU]	CLUSTALV multiple sequence alignment
	[PHY]	PHYLIP phylogenetic inference package version 3.5
	[TREETOOL]  Treetool (X terminals only)
	[PRI]		PRIMER design
	[MAILFASTA]	send a sequence for comparison with sequence databases
	[HELP]		Index Help files

Main Menu[MAINT] Databses&Biogophers[DB] Internet[INT] Directory browser []
 ?)help e)edit	!)unix q)quit, arrow keys to navigate/select, RETURN selects.
-----------------------------------------------------------------------
		 | Welcome to HYGCGmenu	 Unix version 1.2 |

			     Editing Sequences	 [edseq]
	        	     Fragment Assembly	 [fragas]
		   	   Restriction Mapping	 [restmap]
		   	   Sequence Comparison	 [seqcomp]
		Database Searching / Retrieval	 [dbsearch]<----- example
	    	    Multiple Sequence Analysis	 [multseqan]
      	      DNA Sequence Pattern Recognition	 [patrecog]
		       RNA Secondary Structure	 [rnasecstr]
		     Protein Sequence Analysis	 [protan]
			   	   Translation	 [trans]
			  	  Manipulation	 [manip]
				       Display	 [disp]
		       Convert Sequence Format	 [seqconv]
		     File Management Utilities	 [util]
	    	    System Manager's Utilities	 [sysutil]

 What is GCGmenu? [whatisgcgmenu] Is gcg on-line? [Startgcg] 
Request  for help  [mailforhelp]
 ?)help q)quit !)Unix, Arrow keys to navigate, RETURN selects,
------------------------------------------------------------------------
		DATABASE SEARCHING / RETRIEVAL

		FastA	[]
		FastA	[]
	  WordSearch	[]
	    Segments	[]
	 QuickSearch	[]
	   QuickShow	[]    (Please set graphics first)
	FindPatterns	[]
	StringSearch	[]
		Names	[]
		Fetch	[]<------------------
		extract	[extract concecutive numbered sequences]
		DataSet	[]
		DBIndex	[]
	  QuickIndex	[]

    Setting Graphics	[disp]
             GCG Help   [DATABASE_SEARCHING]
   ?)help   !)UnixCommand    Directory browser []
--------------------------------------------------------------------------



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