TMbase -- an announcement

Kay Hofmann khofmann at isrec-sun1.unil.ch
Tue Jul 5 09:58:49 EST 1994

To anyone who is interested in transmembrane proteins:

I would like to announce the availability of TMbase, a database that 
collects information on transmembrane proteins and their (helical) membrane 
spanning domains. 
I originally constructed TMbase as a tool for testing and improving membrane
protein prediction schemes. I planned to include much more useful information
and to make several improvements to TMbase before making it available.

Unfortunately, I am lacking the time to invest much work into TMbase.
Several people encouraged me to believe that the data collection might be
useful even in its present, unfinished state. Thus I decided to make TMbase
available by ftp instead of keeping it in some dusty corner of my file system.

I hope that it is not completely useless.
I included an excerpt from the README file below.

With best regards,

Kay Hofmann

--------------------------- from the README file -----------------------------

TMbase - what is it?

TMbase is a database of transmembrane proteins and their helical membrane-
spanning domains. 
TMbase was originally meant as a tool for analyzing the properties of 
transmembrane proteins. It is intended to facilitate the following tasks:

- finding positional preferences of certain amino acids 
- deriving an improved method for the prediction of transmembrane domains
- testing of such prediction schemes
- statistical testing of general hypotheses concerning transmembrane proteins 

TMbase is mainly based on SwissProt, but contains informations from other 
sources as well. All data is stored in different tables, suited for use with 
any relational database management system. These tables are distributed as 
ASCII files. Since the creation and internal maintenace of TMbase is done on 
a PC using MS-ACCESS, the ACCESS version of TMbase is available as well.

The current release of TMbase (TMbase25) is based on SwissProt release 25.
It has been briefly described in the meeting abstract:

K. Hofmann, W. Stoffel
TMBASE - A database of membrane spanning protein segments
Biol. Chem. Hoppe-Seyler 374,166 (1993)

The data stored in TMbase contain, among other things, information on the

- What SwissProt entries are transmembrane proteins?
- How many transmembrane domains do they possess?
- Where in the sequence are the TM-domains located?
- What is the sequence of the (putative) membrane-buried parts?
- What is the sequence of the flanking regions?
- What is the putative orientation of the transmembrane proteins?
- What is the putative orientation of the TM-helices?
- To what type of membrane are the proteins associated?
- To what species/taxonomic group do the proteins belong?
- What transmembrane proteins are related to another?
- What is the 'relative degeneracy' of a TMbase entry?

all these data are present in a form that can be easily queried.
For a more detailed description of the file structures, see the 
paragraphs below.

Most of the SwissProt-based information has been extracted from theSwissProt 
annotation in a semi-automatical manner. If there are any errors in these 
annotations, they will probably be propagated in TMbase, too. 
However, some consistency checks have been performed though, and in the case 
of any inconsistencies the contradictory information has not been included
into TMbase.
It should be noted, that errors in the annotation of transmembrane helices
are quite frequent since this reflect only the uncertainty of TM-domain
prediction and the lacking of experimental data.

The methodology for grouping the transmembrane proteins into families and
for calculating the 'relative degeneracy' is explained in the paragraphs below.


---- section deleted ----

Considerations of TM-protein Families and Degeneracy

---- section deleted ----


At the moment, TMbase25 is available by anonymous ftp from ulrec3.unil.ch
This address is likely to change in the future.

How to contact the author
If there are any further questions , feel free to contact the author under
this address:

Kay Hofmann
Bioinformatics group
Chemin des Boveresses 155
CH-1066 Epalinges s/Lausanne
FAX: +41 (21) 652-6933
Email: khofmann at isrec-sun1.unil.ch

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