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From: BAIROCH@CGECMU51.BITNET (Amos Bairoch)
Newsgroups: bit.listserv.info-gcg
Subject: PROSITE
Message-ID: <INFO-GCG%90020616595706@UTORONTO.BITNET>
Date: 6 Feb 90 21:58:00 GMT
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              Discussion" <INFO-GCG@UTORONTO>
Reply-To: Amos Bairoch <BAIROCH@CGECMU51>
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<        I, too, am interested in consensus sequence databases. I have a
<document from EMBL called "PROSITE: A dictionary of protein sites and
<patterns" which seems to have quite a lot of work put into it, but it has
<two major problems. First, it is hardcopy (very disappointing for something
<from the EMBL biocomputing group), and second, it has no table of contents
<or index. So far I haven't managed to find a listing for signal peptides.
<
<        If anyone knows of a source of consensus sequence information in
<computer-readable form, could they please post a message to this list?
<
<
<Stephen Clark
<
<clark@mshri.utoronto.ca  (Internet)
<sinai@utoroci            (Netnorth/Bitnet)


In November I have posted to this list (as well as other lists) a news
bulletin that explained that, while release 4 of PROSITE is available,
in a printed form, future releases will be distributed in a computer
readable form.

In fact PROSITE has been all along available in a computer form, in my
sequence analysis package (PC/Gene), but as I have now decided to make
the data bank public domain, I had to define a new distribution format,
it was not possible to do so for release 4.

So before flaming on the fact that it is "very disappointing for something
from the EMBL biocomputing group"  it would be nice if the info that's
available on the net was read. Furthermore the introduction of the PROSITE
book says that:

"This dictionary will very soon be available, on-line, in Europe on the
 EMBL Data Library file server, and in the U.S.A. on the GenBank on-line
 service computer facility."

---------------------------------------------------------------------

<it has no table of contents

There is a table of contents (pages 5 to 9).

---------------------------------------------------------------------

<So far I haven't managed to find a listing for signal peptides.

And you will never see one in PROSITE, signal peptides are not found using
consensus patterns, but using a matrix (profile) approach, as implemented
in the very reliable method of von Heijne [1] which is available in the
majority of sequence analysis packages.

[1] Von Heijne G.
    A new method for predicting signal sequences cleavage sites.
    Nucleic Acids Res. 14:4683-4690(1986).

In addition to von Heijne, there have been three other publications
that describe methods to find signal peptide similar or based on that
method.

Folz R.J., Gordon J.I.
Computer-assisted predictions of signal peptidase processing sites.
Biochem. Biophys. Res. Commun. 146:870-877(1987).

Pascarella S., Bossa F.
CLEAVAGE: a microcomputer program for predicting signal sequence cleavage
sites.
CABIOS 5:53-54(1989).

Popowicz A.M., Dash P.F.
SIGSEQ: a computer program for predicting signal sequence cleavage sites.
CABIOS 4:405-406(1988).
The program for this method is available on the EMBL file server
(get dos_software:SIGSEQ$.UUE)

---------------------------------------------------------------------

<        If anyone knows of a source of consensus sequence information in
<computer-readable form, could they please post a message to this list?

PROSITE release 5.0, will be available on the EMBL file server somewhere
in March.

*****************************************************************************
* Amos Bairoch                * Email: bairoch@cgecmu51                     *
* Dept. Medical Biochemistry  * Tel  : +(41 22) 61 84 92                    *
* CMU                         ***********************************************

* 1, rue Michel Servet        *                                             *
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