CLEVER version 3.03 Available
-----------------------------
This is a notification that the latest version of CLEVER, the Command Line
Entrez VERsion, is now available. CLEVER 3.03 supports searching of the
Entrez databases by the new "date" field using either CDROM (clever) or
network (nclever) Entrez databases.
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 browser, written by NCBI, is a tool that uses
windows, menus, and a pointing device; since not everyone has access
to computers or terminals with graphics capabilities, clever was
developed so that the same queries could be made using only text as
input and 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). See the README file
supplied with the toolkit for a list of these systems.
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 at the following URL:
gopher://megasun.bch.umontreal.ca:70/11/CMB/Entrez/Clever
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. Please see the detailed installation
instructions accompanying these files.
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 Program
at the Universite de Montreal:
ogmp at bch.umontreal.ca
All feedback welcome.
Reference
~~~~~~~~
Rioux, P.A., Gilbert, W.A. and Littlejohn, T.G. (1994)
A Portable Search Engine and Browser for the Entrez Database.
J. Comp. Biol. 1(4): 293-295
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
his assistance.
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, succursale Centre-ville
Montreal (Quebec), H3C 3J7
CANADA
==============================================================================
