"Other Tools" is a very broad category, and I'm not going to spend much time
here. I will briefly mention some other Web-based tools, one Macintosh program
and several e-mail servers (for those without full internet access).
A. SRS
The GCG program LOOKUP is actually an implementation of the Sequence Retrieval System (SRS) created by Dr. Thure Etzold [CABIOS 9(1); 49-57 (1993)].
- SRS can be accessed over the WWW from a server in the Skirball Institute here at NYU-MC:
http://saturn.med.nyu.edu/srs/srsc .
- Similar to ENTREZ, sequences found in an SRS search must be copied from
your WWW browser into a text file on your desktop computer, and then
transferred to your RCR account for further work with GCG.
B. MacVector
- MacVector is a rather sophisticated stand-alone molecular biology package
for the Macintosh computer.
- MacVector can make a direct internet connection to the ENTREZ database. Sequences, once retrieved by MacVector are loaded directly into a sequence
editor window where they are ready for any operation.
- The RCR has a site licence for MacVector, so any lab with an RCR account may
borrow the installation disks and load the program onto their own Mac.
E-mail servers
Each of the major databases has some form of e-mail access to make sequences
available to researchers who do not have full access to the internet with
a graphical WWW browser.
C. NCBI retrieve
- There is an e-mail sequence retrieval service at NCBI that is at times more convenient than interactive access.
Mail your inquiry to
retrieve@ncbi.nlm.nih.gov with the following example format for your query.
DATALIB gb TITLES MAXDOCS 30 BEGIN BOVPRL J02459 [ACC]
- The DATALIB must be on of the following: gb (GenBank),
e (EMBL), sp (Swiss-Prot), pir , or vector
- TITLES will display only the title of the matching record
- MAXDOCS restricts the volume of returns.
- Only DATALIB and BEGIN are mandatory.
- This retrieval service permits Boolean searches. A logical OR is the default.
D. CLEVER.
- The NCBI also provides a program known as CLEVER (Command-Line ENTREZ VERsion). This is a tty-based version of NCBI's ENTREZ
program. It is an interactive tool that allows easy browsing of the ENTREZ
database using only text input/output.
- The CLEVER program also permits BATCH access to the ENTREZ
databases. Thus by use of script files, CLEVER can be integrated as a "search engine" for other applications.
E. EMBL Get
-
The DB GET system is run out of Japan (the Supercomputer Laboratory
(SCL) in Kyoto and the Human Genome Center (HGC) in Tokyo) but is licensed by
the European Bioinformatics Institute.
-
This system allows access by e-mail, gopher, WWW, and the special client program called NetDBget which can be obtained by anonymous FTP
-
EMBL sequences can be obtained via an e-mail message send to the databases
at netserv@ebi.ac.uk.
-
The subject line of an e-mail message should be blank and in the interior of the message put:
get nuc:pip03xx get nuc:x03392 get prot:kap_yeast
-
This will get the sequence with accession numbers pip03xx and x03392 from the
nucleotide databases and the protein sequence with locus name kap_yeast from
the protein database.
F. Others
- Many other databases have specialized access tools, know as clients, that
can provide access to special types of data or unique functions.
- However, as the WWW becomes more sophisticated, more and more of these
functions are being integrated with a Web browser.
- For example the PDB database supports their own PDB Browser. This can be
accessed via the internet or via a downloaded copy that will run on your
own computer.
-
For each database look for a specialized browser (either a WWW site or a custom
program to run on your computer) that allows enhanced access to the data making use of the peculiarities of that database.
- If you are not sure what database to be searching try the very capable WWW search launcher from the Baylor College of Medicine, Houston.
