Ideas and suggestions for *the* yeast database

Francis Ouellette francis at azalea.nlm.nih.gov
Thu Sep 9 04:51:41 EST 1993


Here is something from Patrick Linder, one of the creators of LISTA.

regards,

f.

--
| B.F. Francis Ouellette  
|
| francis at ncbi.nlm.nih.gov   

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Here some comments on the yeast databases.

We have putting together a yeast database containing only protein coding
sequences (Mosse et al., Curr. Genetics 23, 66-91).

The main problems are:

	- different sequences have the same name
	- the same sequences have different names
	- the names often correspond not to the list of R.K. Mortimer
	- the sequences often diverge, due to polymorphisms or sequencing
	  mistakes

For multiple names we have introduced a  "priority rule": The sequence
which was published first gives the name (as far it is acceptable by the
genetic nomenclature) and the names attributed to allelic sequences are given
as synonyms. This is not always satisfactory and may lead to conflicts 
with the genetic nomenclature. But a rule had to be established, otherwise
we never get out of the jungle of gene names. In the future, synonyms which 
have been given from genetic work have also to be included.

We have put all these elements together and release 3 of ListA (1400 entries)
will be published in the upcomming volume "The Yeasts" (Vol 6 "Yeast 
Genetics" Ed.Wheals, Rose and Harrison, Academic Press). It will also soon be
available on bioftp.unibas.ch. 

The yeast database LISTA3 can be used as a flatfile on any personal computer
or can be installed on mainframe computers. We have the ListA database
connected through the SRS system with the EMBL and Genbank databanks.

At present we are also including pointers to Swissprot, Chromosomes and 
overlaps with neighbouring sequences. The next will be the function of 
the genes.

We are always very grateful for corrections and helpful comments.


For the authors:

Patrick Linder
Dept. of Microbiology
Biozentrum
Klingelbergstr. 70
4056 Basel/Switzerland
Fax +41 61 267 21 18
Email linder at urz.unibas.ch



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