CLEVER (Command Line Entrez) Ver. 2.00 Available

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Fri Jun 17 10:33:28 EST 1994


CLEVER version 2.00 Available
-----------------------------
The latest version of CLEVER, the Command Line Entrez VERsion, is now
available by gopher and ftp.  CLEVER 2.00 has 2 major changes since the
the previous release of CLEVER; it now permits access to the taxonomy
information that first appeared in release 10 of the Entrez Database.
In addition, CLEVER now permits more powerful boolean search capabilities
(specifically the NOT function).

Further information about CLEVER, including how to obtain and install
the package, is attached below.



CLEVER- Command line Entrez
---------------------------

What is it?
~~~~~~~~~~~

  clever is a character based version of NCBI's Entrez program. It is an
  interactive tool that allows easy browsing of the Entrez database.

  Entrez is:

     "a molecular sequence retrieval system developed at the
     National Center for Biotechnology Information (NCBI), a division of
     the National Library of Medicine (NLM).  Entrez provides an integrated
     approach for gaining access to nucleotide and protein sequence
     information, to the MEDLINE citations in which the sequences were
     published, and to a sequence-associated subset of MEDLINE.The sequence
     records are derived from a variety of database sources, including
     GenBank, EMBL, DDBJ, PIR, SWISS-PROT, PRF, and PDB.  With Entrez and a
     personal computer, you can rapidly search several hundred megabytes of
     sequence and literature data using techniques that are fast and
     intuitive."
             - Entrez User's Guide.

  The original Entrez program written by NCBI is a tool that uses
  windows, menus, and a pointing device; since not everyone
  has computers or terminals with graphics capabilities, clever was
  written to do the same work using only text input/output.

  In addition, the clever program permits BATCH access to the Entrez
  databases. Thus by use of script files, clever can be made to perform
  queries in batch mode.  In this way clever can be used as a "search
  engine" for any application which has as its input a set of database
  queries in clever format and can use as output any of the data in the
  Entrez databases (in any of the various formats supported by Entrez).

  clever comes in two flavors, "clever", which runs off local Entrez
  databases (e.g. on CD-ROM) and "nclever", which uses the network Entrez
  databases.


Platforms/Operating Systems
~~~~~~~~~~~~~~~~~~~~~~~~~~~

  clever will run on any hardware/operating system combination that
  are supported by the NCBI toolkit (for more information on the NCBI
  toolkit, send an email to toolbox at ncbi.nlm.nih.gov; for more information
  on Entrez, send mail to entrez at ncbi.nlm.nih.gov).  Presently this includes
  (from the README file supplied with the toolkit):

		* IBM 370
		* SUN (SunOS & Solaris)
		* DEC Alpha under OSF/1
		* DEC Alpha under AXP/OpenVMS
		* Macintosh A/UX
		* Microsoft Windows
		* DOS
		* CenterLine CodeCenter
		* Cray
		* Convex
		* Hewlett Packard
		* NeXT
		* IBM RS 6000
		* Silicon Graphics
		* ULTRIX
		* VAX/VMS

  Binaries for clever are supplied for some of these paltform/OS combinations.
  See the relevant "Binaries" directory (see "Obtaining Clever" below).

    
Obtaining Clever
~~~~~~~~~~~~~~~~

  clever can be obtained by gopher by pointing your gopher client at:

	megasun.bch.umontreal.ca

  and selecting:

	 -->  5.  Computational Molecular Biology- programs, documents, help/
 	  -->  9.  Entrez/
	   -->  1.  Clever- Interactive Command Line Entrez/

  or by anonymous ftp to:

	megasun.bch.umontreal.ca

  Files can be retrieved from the /pub/clever directory.


Installation Instructions
~~~~~~~~~~~~~~~~~~~~~~~~~

  There are two options for installing clever on your system.  The
  first is to obtain the code and compile it on your own system.
  obtain the cleverXXX.tar (where XXX is the current version number)
  from the Distribution directory in the repositories discribed above.
  Then read the INSTALLATION file in that directory.

  The second is to obtain precompiled executable files.  Executables
  for some platforms are supplied in the Binaries directory located
  in the repositories described above.  The files are named by their
  version number; be sure to remove this number before using them.
  You also need to make sure you have an appropriate ncbirc file
  available.  For unix systems, this will be a file called .ncbirc
  and be located in your home directory.  See the Entrez documentation
  for details on configuring entrez on other computer platforms.
  A sample ncbirc file is provided in the Documentation directory.

  Note that to use clever you will need access to the entrez databases
  locally (e.g. on CDROM), and for nclever, you will need access to
  the Entrez databases at NCBI through the Internet.  Send mail to
  entrez at ncbi.nlm.nih.gov for more information on obtaining the Entrez
  databases.


Further Information
~~~~~~~~~~~~~~~~~~~

  For more information about the clever project, send email to the
  Informatics Division of the Organelle Genome Megasequencing Unit
  at the Universite de Montreal:

	ogmp at bch.umontreal.ca

  All feedback welcome.


Credits
~~~~~~~

  This software was written by Pierre Rioux of the OGMP (Organelle
  Genome Megasequencing Project), Departement de Biochimie, Universite
  de Montreal (riouxp at bch.umontreal.ca) and William A. Gilbert, of
  the University of New Hampshire (gilbert at unh.edu) under the management of
  Tim Littlejohn, OGMP, Departement de Biochimie, Universite de Montreal
  (tim at bch.umontreal.ca).  Please send any comments/correspondence to
  ogmp at bch.umontreal.ca.  Thanks also to Jonathan Epstein at NCBI for
  providing some of the binary files of clever & nclever.
      
  The development of clever was supported by a grant from the Canadian
  Genome Analysis and Technology Program (CGAT).

-- 
==============================================================================
Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
            C.P. 6128, Centre-ville
            Montreal (Quebec), H3C 3J7
            CANADA
==============================================================================




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