ListA4

Reinhard Doelz doelz at comp.bioz.unibas.ch
Wed May 24 06:50:33 EST 1995


The SDL files for LISTA are available  at the sources mentioned below.
Regards
Reinhard 





[ Article crossposted from bionet.molbio.yeast ]
[ Author was patrick linder ]
[ Posted on 24 May 1995 10:09:23 +0100 ]



Dear Netters,


We are happy to announce the release of ListA4.1. The document which 
follows has been extracted (and shortened) from lista.doc describing 
the database. Please refer to the original document for full documentation.


For comments, informations and suggestions, please contact:
Patrick Linder, Dept. of med. Biochemistry, CMU, 1, rue Michel Servet, 
1211 Geneva, Switzerland

Tel +41 22 - 702 54 84
FAX +41 22 - 702 55 02
Email: linder at cmu.unige.ch




=======================================================================
LISTA, Release 4.1, March 1995

A comprehensive compilation of nucleotide sequences encoding proteins 
from the yeast Saccharomyces


      Doelz, R., Mosse, M. O., Slonimski, P. P., Bairoch, A.
      and Linder, P. (1994). LISTA, LISTA-HOP and LISTA-HON: a 
      comprehensive compilation of protein encoding sequences 
      and its associated homology databases from the yeast 
      Saccharomyces. Nucleic Acids Res. 22, 3459-3461.



3.2.1 NEW DATA FIELDS IN RELEASE 4

The CL field (chromosomal localization) was added in order to indicate
where the gene has been localized. The AC field (accession number) was
added, one for each entry. Note that the accession numbers start with SC
(for Saccharomyces Cerevisiae). Access ion numbers introduced in the
interim release 3.1 were dropped, to account for the principle of one
accession number per gene rather than one per quoted reading frame. The DT
field has been added to facilitate maintenance. . 

3.2.2 CROSS-REFERENCESTO THE SWISS-PROT DATABASE 
Since release 4.1 an effort has been made to
include all the entries in SWISS-PROT and to introduce a DR field for
crossreference with Swissprot. This supplements the functionality as
already present earlier as via the SWSS-PROT database is immediately 
linked to the corresponding MEDLINE reference quotation via the SRS system
(see below). 



3.4 GROWTH 

LISTA 4.1 contains data from 1909 sequences,corresponding to 1420 genes
and 376 synonyms. The exact growth curve is shown below: 

LISTA 1      400 genes and synonyms
LISTA 2      811 genes, 125 synonyms, 1001 sequences
LISTA 3     1127 genes, 176 synonyms, 1400 sequences
LISTA 4.1   1420 genes, 376 synonyms, 1909 sequences 


4 NOMENCLATURE

Genetic nomenclature relies on the glossary compiled by [6] and was used
whereever possible. In many cases, however,no or incorrect gene
designations have been given to published sequences.Moreover,the same name
was given to different sequences or differen t names have been given to
the same sequence. To sort out this problem of nomenclature a priority
rule for naming genes in the present database [2] was established.
According to this rule the name of the first pub- lished sequence (date of
acceptance of th e publication) is used in the list, provided it is in
accordance with the standard genetic nomenclature.Other names are included
as synonyms. In some cases four letter designations (ARGR1,MRPL20) or gene
names followed by a letter (RPL4A, TIF51A) have als o been used. In the
case of historically well established gene designations such as HO,it was
self- evident that they should be retained. 

Although these rules are straight and easy to handle, in some cases this
leads to the use of names which are no longer in use. In such cases the
currently used name is given and the "historical" name is given as
synonym. 


6 STATUS OF THE DATABASE

6.1. AVAILABILITY 

The LISTA database is available either by anonymous FTP from
bioftp.unibas.ch [131.152.8.1] in the archive_data/lista directory or its
mirror ftp.switch.ch [130.59.1.40] in the
mirror/embnet-ch/archive_data/lista directory on the internet. New
sequences a nd comments on the existing database may be sent to P. Linder
(linder at cmu.unige.ch). LISTA is distributed by the EMBL data library and
the associated services (CD-ROM, FTP, EMAIL servers). 

ListA can also be queried using the SRSWWW system on one of the
corresponding servers, e.g. http://www.ch.embnet.org/srs/srsc. 


6.2. FUTURE (INCREMENTAL) RELEASES

Further releases are still open for feed-back and suggestions, and it is
suggested to contact linder at cmu.unige.ch for comments and desired
enhancements.

An effort will be made to add new entries to the existing list
without any announcement. The new entries will be available in Lista4_new.


6.3. ADDITIONS: HOMOLOGY CALCULATIONS

The LISTA database does not currently contain any sequence data from
entries available in the EMBL data library. Experimental versions of an
EMBL-formatted file which includes sequence data are available as
LISTA-HON (the homologies on the Nucleotide leve l) and LISTA-HOP (the
homologies on the Protein level). The release of ODD files describing the
LISTA , LISTA-HON and LISTA-HOP format for parsing into the SRS system [7]
is experimental at this point of time and suggestions are most welcome to
doelz at ch.e mbnet.org (Reinhard Doelz, address see above). 


6.4. FILES FOR USE IN THE SRS SYSTEM

The SDL files to be modified are srsdb.sdl, hyperlink.sdl and lista.sdl. 
The latter is provided as part of the distribution. For proper
integration, do the following additions similar to the example: 
(lines without : are wrapped for ease of reading) 



7 ACKNOWLEDGEMENTS

We are very grateful to all those, who have provided input in solving
nomenclature problems and giving informations on inconsistencies. We would
also like to thank Thure Etzold for assistance in building the LISTA.SDL
file.This work was supported by grants from the Ministere de la Recherche
et de l'Espace (program GREG; P.S.), from the Swiss National Science
Foundation (R.D. and A.B), the University of Basel (R.D. and P.L) and the
University of Geneva (P.L.  and A.B.). We are very grateful to S.
Brouillet, J.L. Risler and the Rechenzentrum of the University of Basel
for help. 




-- 
 R.Doelz         Klingelbergstr.70| Tel. x41 61 267 2247  Fax x41 61 267 2078|
 Biocomputing        CH 4056 Basel| electronic Mail    doelz at ubaclu.unibas.ch|
 Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
<a href=http://beta.embnet.unibas.ch/>EMBnet Switzerland:info at ch.embnet.org</a> 




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