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.
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@ncbi.nlm.nih.gov ; for more information on Entrez, send mail to entrez@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).
Clever is available by anonymous ftp to:
Files can be retrieved from the /pub/clever directory.
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@ncbi.nlm.nih.gov for more information on obtaining the Entrez databases.
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.
For more information about the clever project, send email to the Informatics Division of the Organelle Genome Megasequencing Unit at the Universite de Montreal:
All feedback welcome.
This software was written by Pierre Rioux of the OGMP (Organelle Genome Megasequencing Project), Departement de Biochimie, Universite de Montreal (riouxp@bch.umontreal.ca ) and William A. Gilbert, of the University of New Hampshire (gilbert@unh.edu ) under the management of Tim Littlejohn, OGMP (current address at ANGIS, Australia: tim@angis.su.OZ.AU). 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).