Database searching

Peter Rice rice at embl-heidelberg.de
Tue May 18 08:03:36 EST 1993


In article <1t88u8INNheo at titan.ucs.umass.edu>, lmegna at titan.ucs.umass.edu (Lisa
Megna) writes:
> How can I search these and other nucleotide and protein sequece databases
> by email?  I am especially interested in searching databases not currently
> avaibale through gcg.  For example, I have heard of a database of random
> sequences of human DNA.

You have several options. The latest database entries are available at many
sites for searching by E-mail. For example, you can send mail with the message
text HELP to the following addresses:

BLITZ at EMBL-Heidelberg.DE - massively parallel protein search program
			   (like BESTFIT in GCG against the whole database)
FASTA at EMBL-Heidelberg.DE - FASTA search of protein or DNA databases
QUICK at EMBL-Heidelberg.DE - GCG QUICKSEARCH (improved version)

other search services are regularly posted to these newsgroups, I expect you
will get their details. BLAST services are especially useful. You should
try both and compare them to BLITZ.

As you have GCG you can also convert any other database to GCG format for
searching. Sometimes you have to modify a GCG program or write a new one, but
you have the full instructions with the package. Let me know if you need help
with this.

I assume the "random human DNA" database is a reference to EST sequencing
efforts which aim to sequence a complete cDNA library. The "random" just
means that a random cDNA is sequenced with no clue yet to its function. These
sequences are already included in the EMBL/GenBank/DDBJ sequence databases,
for human and for several other organisms.

If there is sufficient demand, the EST sequences could be made available for
searching separately by our search services - they are certainly "different"
in that they may contain sequencing errors and their annotation is limited
by the lack of biological knowledge.

 -----------------------------------------------------------------------------
 Peter Rice, EMBL                             | Post: Computer Group
                                              |       European Molecular
 Internet:    Peter.Rice at EMBL-Heidelberg.DE   |            Biology Laboratory
                                              |       Postfach 10-2209
 Phone:   +49-6221-387247                     |       W-6900 Heidelberg
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