©
1996 Oxford University Press
50-52
Footnote
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and
its associated homology databases from the yeast
Saccharomyces
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces
Reinhard
Dölz
,
Marie-Odile
Mossé
1
,
Piotr P.
Slonimski
1
,
Amos
Bairoch
2
and
Patrick
Linder
2,
*
Biocomputing, Biozentrum, Klingelbergstraße 70, 4056
Basel
,
Switzerland
,
1
Centre de Génétique Moléculaire, Laboratoire propre du CNRS associé à l'Université Pierre et Marie Curie, F-91190
Gif sur Yvette
,
France
and
2
Dept. de Biochimie médicale, Centre Médicale Universitaire, 1, r. Michel Servet, 1211
Genève
4,
Switzerland
Received November 6, 1995
;
Accepted November 15, 1995
ABSTRACT
We continued our effort to make a comprehensive database (LISTA) for the yeast
Saccharomyces cerevisiae
. As in previous editions [Dölz,R., Mossé
,
M.-O., Slonimski, P.P., Bairoch,A. and Linder,P. (1994)
Nucleic Acids Res
. 22, 3459-3461] the genetic names are consistently associated to each sequence with
a known and confirmed ORF. If necessary, synonyms are given in the case of
allelic duplicated sequences. Although the first publication of a sequence
gives-according to our rules-the genetic name of a gene, in some instances more commonly used
names are given to avoid nomenclature problems and the use of ancient
designations which are no longer used. In these cases the old designation is
given as synonym. Thus sequences can be found either by the name or by synonyms
given in LISTA. Each entry contains the genetic name, the mnemonic from the
EMBL data bank, the codon bias, reference of the publication of the sequence,
Chromosomal location as far as known, SWISSPROT and EMBL accession numbers. New
entries will also contain the name from the systematic sequencing efforts.
Since the release of LISTA4.1 we update the database continuously. To obtain
more information on the included sequences, each entry has been screened
against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. This release includes reports from full Smith and
Watermann peptide-level searches against a non-redundant protein sequence database. The LISTA data base can be
linked to the associated data sets or to nucleotide and protein banks by the
Sequence Retrieval System (SRS). The database is available by FTP and on World
Wide Web.
LISTA, a compilation of coding sequences
In view of the very rapid growth of sequence data from genetic and biochemical
experiments and systematic sequencing we continued to compile a list of coding
sequences from yeast (
1
-
4
). The database contains sequences from
Saccharomyces cerevisiae
,
Saccharomyces
carlsbergiensis
and
Saccharomyces
uvarum
, which are believed to constitute conspecific taxonomic species (
5
). Likewise, sequences from
Schizosaccharomyces pombe
,
Candida
,
Hansenula
and others are not included. Not included are sequences from extragenomic
nuclear elements, mitochondria and Ty elements. The actual list (LISTA4.1)
contains 1461 sequences and 349 synonyms from 1386 individual protein
sequences. It has been updated in 1994 to include cross-references to the SWISSPROT database. Since release LISTA4.1 the database
is updated continuously.
Data from the systematic sequencing of the yeast genome are only included if
they have a defined function or a homologous sequence in the data banks. New
entries since LISTA4.1 contain a SN entry field with the ORF designation from
the systematic sequencing. Unidentified open reading frames are not considered.
The database includes at present a gene name and a unique accession number. The
date field (used for administrative purposes) is followed by a cross-reference to the SWISSPROT database and the chromosomal location (if
known). Each known DNA sequence is listed afterwards, with a synonym in the
case the same sequence has been published more than once under different names.
The mnemonic, the length of the coding sequence without the stop codon, the
codon bias according to (
6
), the reference of the first publication of the sequence and the accession
number of EMBL are listed for each entry. In the case of conflicting sequence
data or nomenclature a commentary is given to point out the divergences. To
increase the information content of databases starting with release 31 of the
SWISSPROT database the entries therein will refer to the LISTA accession
numbers to facilitate communication between the two.
A major problem in establishing such a database is the nomenclature. We tried
whenever possible to follow the genetic nomenclature and follow the glossary
compiled by (
7
). 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 different names have been given to the same sequence. To sort out this
problem of nomenclature we use the name of the first published sequence (date
of acceptance of the publication), provided it is in accordance with the
standard genetic nomenclature (
2
). In the case of historically well established gene designations such as
HO
, it was self-evident that they should be retained. In some cases an original gene name
is no longer used in the current literature, but a new designation (sometimes
more reasonable) has been adopted. In these cases we adopt the new gene name,
but give the original name as synonym. An effort is undertaken to provide a
nomenclature consistent with SWISSPROT and the SGD database.
Duplicated sequences from the same gene or non allelic sequences from duplicated
genes can be distinguished by comparing the 5' and 3' non-coding sequences, which in general diverge considerably in
non allelic duplicated genes but are highly similar or identical in allelic
sequences. Exceptions have been discussed (
2
). In both cases, the results of the comparisons are included in the commentary.
Each entry in the database is composed of lines which are listed in Table
1
. An example has been shown previously (
8
). This arrangement of the database allows an easy integration with other data
bank. Links between the LISTA database and the SWISSPROT and EMBL sequence data
library were accomplished using the Sequence Retrieval System program (
9
). The database is also accessible on the World Wide Web
(http://www.ch.embnet.org/) or by using SWISSPROT at Expasy
(http://expasy.hcuge.ch/).
Table 1
.
Format of the LISTA database in electronic form
|
Number of fields
|
Key
|
Description
|
|
always 1 (begins each entry)
|
GN
|
Gene name
|
|
always 1
|
AC
|
LISTA accession number
|
|
0 or more
|
SY
|
Synonym
|
|
1 or more per GN or SY
|
DR
|
Data references to either EMBL, SWISSPROT, LISTA-HON or LISTA-HOP
|
|
1 per DR
|
SN
|
Name from systematic sequencing (since release 4.1)
|
|
1 per DR
|
LN
|
Length of sequence
|
|
1 per DR
|
CB
|
Codon bias
|
|
1 per DR
|
RL
|
Literature reference
|
|
1 or more
|
DT
|
Date information for maintenance
|
|
0 or more
|
CC
|
Additional comments
|
|
1 per entry
|
//
|
End of entry
|
Data from sequence homology screening improved
The open reading frames collected in the LISTA4 database have been translated
into protein sequences, and were screened against a non-redundant protein sequence database collections composed with the `nr'
program from NCBI (Gish, W. , National Center for Biotechnology Information,
Bethesda, USA, software published on FTP server). In addition to the SWISSPROT
and PIR databases, the automatically translated EMBL entries as compiled by the
SRS program (
9
) were added, thus expanding the scope of the data used for comparison. The
algorithm employed for protein searches was a full Smith and Watermann search
as implemented in the MPSRCH program running on a MasPar supercomputer with
4096 processors. As the databases grow rapidly, we will update this homology
screening database frequently.
Additionally, DNA sequences were subsequently screened against a non-redundant DNA sequence database collections composed with the same tool as
described above, covering EMBL and GenBank DNA sequence databases including
updates.
The blastn and MPsrch programs, respectively, were used to obtain top-scoring sequences with a significant homology (
10
,
11
). To make the output more versatile, the output of the screening process was
post-processed to give one line of description per sequence found, and one line
per matching segment pair. Arbitrary but reasonable cut-offs (probability <10 e
-30
or >60% identity for blast, probability < 10
-100
for MPsrch) were applied to list only entries which are believed to be most
significant. The entry codes (for a format description, see Table
2
) reflect the fact that multiple reading frames can occur in the same sequence.
If this is the case, the number of the reading frame is part of the ID, e.g.
ENTRY-1 would designate the ORF 1 of the entry ENTRY. As LISTA and LISTA-HOP are plain flat files containing cross-references to the sequence databases, the linkage between
LISTA, LISTA-HON and LISTA-HOP can be achieved using a sequence retrieval program which is
capable of utilizing this information. We have successfully used the Sequence
Retrieval System SRS (Etzold
et al
.), which is available in the public domain, and also accessible on public
servers on the Internet.
Table 2
.
Format of the LISTA-HON and LISTA-HOP database, respectively, in electronic form
|
Number of fields
|
Key
|
Description
|
|
always 1(begins each entry)
|
ID
|
Gene name
|
|
1 per entry
|
DE
|
Description
|
|
1 per entry
|
DR
|
Reference to LISTA database
|
|
1 per entry
|
DT
|
Last change of entry
|
|
1 per entry
|
GN
|
Gene name
|
|
1 or more per entry
|
HY
|
Homology found
|
|
1 or more per HY
|
HD
|
Description of Homology
|
|
1 per entry
|
HN
|
Name of top homologous sequence as derived from database
|
|
0 or more
|
XX
|
Placeholder
|
|
0 or more
|
CC
|
Additional comments
|
The much enhanced sensitivity of the MPsrch program, paired with statistically
based threshold limitation, allows to list even remotely related sequences.
This is in particular useful to classify families of genes with respect to
interspecies homology. In combination with the SRS Program, it is possible to
reverse the usage of the link: given a vertebrate sequence, it is possible to
look up this entry in either LISTA-HON or LISTA-HOP to query LISTA for a similar gene in
Saccharomyces cerevisiae
based on sequence homology.
The LISTA, LISTA-HOP and LISTA-HON databases are available by anonymous FTP from
bioftp.unibas.ch
(131.152.8.1) or are accessible on the World Wide Web (
http://www.ch.embnet.org/
) or by using SWISSPROT at Expasy (
http://expasy.hcuge.ch/
).
ACKNOWLEDGEMENTS
This work was supported by grants from the Ministre 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 the University of Geneva
(A.B and P.L.). We are very grateful to the Rechenzentrum of the University of
Basel for help.
REFERENCES
1 Mossé, M.O., Brouillet, S., Risler, J.L., Lazowska, J. & Slonimski, P.P. (1988) Curr. Genet. 14, 529-535. MEDLINE Abstract
2 Mossé, M.-O., Linder, P., Lazowska, J. & Slonimski, P.P. (1993) Curr. Genet. 23, 66-91. MEDLINE Abstract
3 Mossé, M.O., Dölz, R., Lazowska, J., Slonimski, P.P. & Linder, P. (1995) In Wheals, A.E., Rose, A.H. & Harrison, S.E. (eds) The Yeasts. Vol. 6, Academic Press, London, pp. 499-582.
4 Dölz, R., Mossé, M.O., Slonimski, P.P., Bairoch, A. & Linder, P. (1994) Nucleic Acids Res. 22, 3459-3461. MEDLINE Abstract
5 Barnett, J.A., Payne, R.W. & Yarrow, D., p.811 Cambridge University Press, Cambridge, 1983.
6 Bennetzen, J.L. & Hall, B.D. (1982) J. Biol. Chem. 257, 3026-3031. MEDLINE Abstract
7 Mortimer, R.K., Contopoulou, C.R. & King, J.S. (1992) Yeast 8, 817-902. MEDLINE Abstract
8 Linder, P., Dölz, R., Mossé, M.O., Lazowska, J. & Slonimski, P.P. (1993) Nucleic Acids Res. 21, 3001-3002. MEDLINE Abstract
9 Etzold, T. and Argos, P. CABIOS 9, 49-57 (1993).
10 Altschul, S.F., Gish, W.G., Miller, W., Myers, E.W. & Lipman, D.J. (1990) J. Mol. Biol. 215, 403-410.
11 Collins, J.F. and Coulson, A.F.W. (1990) Methods Enzymol. 183, 474-487. MEDLINE Abstract
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*
To whom correspondence should be addressed
