ANNOUNCE: rncbi2 graph. frontend to BLAST, EMBL, NCBI services

Sebastian Bunka unknown at i112syw1.vu-wien.ac.at
Thu Sep 21 02:52:29 EST 1995


ANNOUNCE

	RNCBI2 version 0.2
	==================
	Graphical frontend program for the retrieval of biological
	database entries from e-mail servers at the NLM/NIH, EMBL, and
	other sites including simple blast analysis requests of DNA and 
	AA sequences at the blast server of NCBI/NIH.


	Software/Hardware requirements
	==============================
	X11R5/6, tcl 7.3, and tk 3.6, should run on any Unix(tm) or
	comparable workstation (developed on an INTEL 486 computer
	running Linux 1.2.8).


	Distribution
	============
	Source code of the interpreted language tcl with tk extensions.
	Complete package is free software (C) by Sebastian Bunka under 
	the terms of the Gnu General Public License.


	Author
	======
	Sebastian Bunka, Institute of Medical Chemistry, University
	of Veterinary Medicine, Linke Bahngasse 11, A-1030 Vienna,
	AUSTRIA. 
	E-mail Sebastian.Bunka at vu-wien.ac.at
	Phone (+43)-1-711 55 306, FAX (+43)-1-713 68 95


	Where to get it
	===============

	You can get the program package from:

	ftp.ebi.ac.uk:/pub/software/rncbi/rncbi2.tar.Z



	from the general information file
	=================================

RNCBI2 - Introduction to RNCBI2
-----------------------------------------------------------

What is RNCBI2
--------------

RNCBI2 is a simple frontend for many biological e-mail database
servers located in several countries in the world. RNCBI1 was
a simple shellscript that allowed me to submit database entry
requests to the retrieve server of NCBI at the NIH. The reason
to write such a thing was that a) after I upgraded my X11 system
to R6 my old GDE didn't work any more and b) I could not find
the manuals of the retrieve service at NIH (and could not
remember how to setup a query).

RNCBI2 was devloped using Tcl 7.3, Tk 3.6, and the XF GUI Builder
from Sven Delmas at the Technical University in Berlin.


QUICK TOUR
----------

When you read this help file, you propably have fired up RNCBI2.
The only useful of the main window are the menus.

((On the left: the heraldic figure of our university. The letters are 
  hard to read so I type it here correctly

    "UNIVERSITAS MEDICINAE VETERINARIAE VINDOBONENSIS MDCCLXVI"))


FILE (some general stuff)

	ABOUT	- Here you'll find my address ;-)

	EDIT/CREATE FASTA file
		- Pops up a file browser and lets you choose
		or create a file and invokes your preferred editor
		on this. FASTA format see the help menu.

	QUIT	- good bye.


COMPOSE (compose your e-mail request)

	NIH Retrieve Server
		- fires up a new window where you can enter keyword(s),
		accession number(s) or logical expressions to be re-
		trieved from the retrieve server at ncbi.nlm.nih.gov.
		It lets you choose to obtain data from a number of
		databases, whether you want only the titles of the
		entries, the number of documents and lines you want
		in the response.

	NIH Blast Server (DNA)
		- fires up a new window where you can select or create
		a DNA sequence to be submitted to be evaluated at the
		blast server using the blastn program. Just choose the
		database, the strand, alignment, expect value and
		number of descriptions. See the BLAST Manual in the Help
		section.

	NIH BLAST Server (Peptide)
		- fires up a new window where you can select or create
		an AminoAcid sequence to be submitted and evaluated at
		the blast server using the blastp program. Just choose
		the database, matrix, and other values. See the BLAST 
		Manual in the Help section.

	Datafile by Accession a'la dbget
		- fires up a new window where you can enter one or more
		accession number and/or entry names and select a database
		where you want the data to be retrieved from.


PREFERENCES (your default settings)

	EDIT LOCAL preferences
		- fires up a new window where you can change your local
		default settings. Most useful if you want to use your
		preferred editor with RNCBI, and have a default data
		path. Or if you want to get all replies from the servers
		to a different e-mail address (does NOT work with 
		ACCESSION). Also you can check if you want to have
		your request carbon copied to yourself (I like that!).
		Or reset to the systems default values.


HELP (If you want to have more questions answered)

	LICENSE
		License of RNCBI2 - its free under the GPL

	RNCBI General
		You're reading it ;-)

	FASTA format (Create)
		explains the format of a FASTA format used with
		the BLAST service.

	Help on RETRIEVE
		the (original) Help manual for the retrieve service
		at the NIH - from the NIH. Gives you useful infor-
		mation on how to select special filds in your re-
		quest and many other information.

	Help on BLAST
		the (original) Help manual for the blast service
		at the NIH - from the NIH. Gives you useful infor-
		mation on how to set special parameters in your re-
		quest (align, expect) and many other information.

	BLAST Manual
		the (original) Blast man page from the NIH. A lot
		of background information.

	Blast FAQ
		Frequently asked questions regarding the blast service.

	Blast Notice
		A note regarding special blast programs not available
		with this front end.




Vienna, September 1995

Cheers, Sebastian


***end of announce***



--

;-)
------------------------------------------------------------------------
Sebastian Bunka			ph. (+43-1) 711 55 301
Institute of			FAX (+43-1) 713 68 95
Medical Chemistry		email: Sebastian.Bunka at vu-wien.ac.at
University of Veterinary Medicine - Vienna - Austria
------------------------------------------------------------------------





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