ABSTRACT
YPD is a database for the proteins of the budding yeast,
Saccharomyces cerevisiae
. YPD has two formats: (i) a spreadsheet which tabulates many of the physical
and functional properties of yeast proteins, and (ii) the YPD Protein Reports
which are formatted pages containing the protein properties, annotations
gathered from the literature, and references with titles. YPD is available
through the World-Wide Web, through an Email server, and by anonymous FTP. New releases of
the YPD spreadsheet are produced every two to four months, and the on-line information is updated daily.
YPD is a protein database specialized in the collection of the physical and
functional information for the proteins of budding yeast
Saccharomyces cerevisiae
. YPD evolved from a project at the QUEST Protein Database Center of the Cold
Spring Harbor Laboratory to identify yeast proteins on two-dimensional gels (
1
,
2
). For this project, knowledge of the predicted isoelectric point, molecular
weight, codon bias, post-translational modifications, subcellular localizations, precursor peptide
lengths, and amino acid composition of mature proteins was needed to assist in
protein identifications. A tabulation of data from the protein sequence
databases and from the literature was begun. The tabulation was made non-redundant by screening multiple versions of each sequence from the
database. YPD has now been expanded into a general resource that is available
(i) as a spreadsheet for downloading into personal computers, (ii) through an
Email server, and (iii) through the World-Wide Web (WWW).
YPD is complementary to other biological databases in content and in format. The
Saccharomyces
Genome Database (SGD), a primary resource for yeast genetic information
maintained by J. Michael Cherry at the
Saccharomyces
Genome Information Resource (
3
) at Stanford University, has links to YPD information through its `protein-info' class. YPD does not contain sequence information, but instead gives
accession numbers to GenBank, SWISS-PROT, and PIR-International. The spreadsheet format of YPD allows users to load
and manipulate the entire database of protein properties and references on a
personal computer. A different format, the YPD Protein Reports, is used for
presentation on the WWW and Email servers. Each YPD Protein Report displays
protein properties, functional annotations, and references for one protein. The
YPD Protein Reports are searchable by gene name, by keywords, and by the
protein property categories.
YPD was first released as a spreadsheet for downloading by anonymous FTP in
November, 1994. New releases of the spreadsheet have been provided every 2 to 4
months. YPD has been available since 1994 on the QUEST World-Wide Web server at the Cold Spring Harbor Laboratory, where it is
interfaced to two-dimensional gel maps through the Global Gel Navigator Software (
2
), and on the
Saccharomyces
Genome Database (SGD) WWW server. The YPD Protein Reports were made available
in 1995 through a new World-Wide Web server and Email server at Proteome, Inc. The YPD database is
maintained at Proteome, Inc. as a free public resource.
The YPD spreadsheet contains one record (row) for each yeast protein of known
sequence, including the open reading frames discovered by systematic genome
sequencing. The identifier for each record is the gene name. The genetic names
for budding yeast are coordinated at the
Saccharomyces
Genome Database at Stanford, using the published literature, the LISTA database
of Patrick Linder (
4
), and direct submissions from investigators. For each record, the YPD
spreadsheet lists the SGD gene name, the SWISS-PROT gene name, and a list of synonyms that includes all known names used
for the gene, including temporary and permanent names assigned by systematic
sequencing.
Accession numbers to GenBank, PIR-International and SWISS-PROT are given as fields in the spreadsheet. When multiple sequences
for a gene are available in the databases, the sequence from systematic
sequencing is selected or, if that is not available, the most recent sequence
is usually selected. Calculations of isoelectric point, molecular weight, codon
bias, codon adaptation index, and amino acid composition, etc. are based on the
designated GenBank sequence. Fragments of N- and C-terminal sequence are given in the spreadsheet to help users verify
the identity of the protein in cases where the nomenclature is confusing.
All calculations of predicted properties, motifs, and amino acid composition are
based on the mature protein sequence after removal of N- and C-terminal precursor peptides. YPD relies on the experimental or
strongly predicted cleavage sites reported in the literature. YPD itself does
not make cleavage site predictions.
The complete list of fields (columns) used in the spreadsheet format of YPD are
listed in Figure
1
.
The YPD Home Page on the World-Wide Web, shown in Figure
2
, provides access to all formats of YPD, including the online search form for
access to YPD Protein Reports, the Global Gel Navigator on the QUEST WWW server
(
2
), the Email server, and the FTP server. It also contains links to pages with
introductory material, documentation, and summaries of the YPD contents. The
YPD Protein Reports are obtained after making selections on the search form by
gene name, by keywords, or by protein property categories.
An example YPD Protein Report is shown in Figure
3
. This format presents 34 fields of data from the spreadsheet, annotations
gathered from the literature, and the reference list with titles. This format
is used to present information for each protein as an Email report or as a
single WWW page. These are recompiled daily so that the latest updates are
always available on-line. In addition, a file containing all the YPD Protein Reports on the
date of the latest spreadsheet release can be downloaded by anonymous FTP (see
below).
The spreadsheet version of YPD is inherently searchable by its categorized
protein properties, however, it must be downloaded to be used and it is does
not contain the functional annotations. The Email and WWW versions have search
forms that allow convenient searching of the YPD Protein Reports by gene name
or synonym, by keywords, and by the protein properties. The form allows `AND'
and `OR' modes for construction of queries based on multiple criteria. These
Email and WWW servers always use data from the latest daily updates. The result
of each search is a page containing a synopsis of the search strategy, and a
list of the protein `hits' by gene name, synonyms, and protein
name/description. On the WWW page, clicking any protein in the `hit' list
brings up the corresponding YPD Protein Report.
Release 4.1 contains 4305 entries including sequences from GenBank through July
30, 1995, SWISS-PROT through May 23, 1995, and PIR-International Release 43. Of these sequences, 3789 derive from
systematic genomic sequencing projects. YPD currently lists 2012 proteins that
have been characterized through genetics or biochemistry, 729 proteins that are
known only by homology to characterized proteins, and 1564 that have unknown
function. In the current release, YPD tabulates 477 nuclear proteins, 249
mitochondrial proteins, 136 transcription factors, 94 protein kinases, 16
cyclins, and many other categories relating the function, localization, and
modification of the proteins. A complete summary of the YPD contents by
category is found in the spreadsheet documentation and under YPD Summaries on
the YPD Home Page.
The spreadsheet data file is just over 3 megabytes in size and the collection of
all YPD Protein Reports is about 13 megabytes in size, although each are
available in compressed format. A summary of the growth of YPD since its
release in 1994 is shown in Table
1
.
Table 1
.
The FTP server contains the spreadsheet data files (YPD_Excel) formatted for
Microsoft Excel on Macintosh and formatted as tab-delimited ASCII text (YPD_ASCII) for loading into any spreadsheet. The
associated files include documentation (YPD.doc), a references file (YPD_REFS),
and a file (YPD_FORMATTED) containing all the YPD Protein Reports. The address
of the FTP server is isis.cshl.org, and the directory is /pub/yeast/YPD. The
FTP server can also be accessed from the YPD Home Page.
The Email server is accessed by sending Email to yeast@ proteome.com. YPD
Protein Reports are requested by placing one or more gene names in the subject
line. The search form is requested by placing `HELP' in the subject line.
Documentation is available by placing `DOC' in the subject line. The YPD
Protein Reports and other documents are automatically returned, with each
report in a separate Email message.
YPD can be reached on the World-Wide Web through the YPD Home Page (http://www.proteome.com/YPDhome.html).
Data from YPD has also been incorporated into the WWW server of the QUEST
Protein Database Center (http://siva.cshl.org/#ypd), the
Saccharomyces
Genome Database (SGD) (http://genome-www.stanford.edu), and the MIPS Protein Database/Yeast Genome Database
(http://www.mips.biochem.mpg.de). The QUEST site is managed by latter{at}cshl.org
(latter@cshl.org), SGD is managed by J. Michael Cherry
(cherry@genome.stanford.edu), and MIPS is managed by mewes{at}mips.embnet.org
(mewes@mips.embnet.org). The implementation of YPD on the MIPS WWW server is
managed by kleine{at}mips.embnet.org (kleine@mips.embnet.org) and harris{at}mips.embnet.org
(harris@mips.embnet.org). The YPD Home Page and the contents of YPD are
maintained by jg{at}proteome.com (jg@proteome.com).
Authors wishing to cite YPD should use this article as a general reference for
the latest release available electronically.
I am grateful to Gerald Latter and Bruce Futcher for discussions that led to the
YPD Project, and to Gerald Latter and Tom Boutell for their pioneering
implementation of YPD on the QUEST WWW server. I thank Michael Cusick, Les
Grivell, Bruno André, Jonathan Warner, and Rick Moerschell for expert review and assistance
with portions of the database. Finally I thank Irene Ong for WWW assistance,
and Rachelle Hecht and Shelley Lengieza for assistance in building YPD, and
Cheryl Lengieza for assistance in preparing the manuscript.
Release
Date
Total
Known
a
Homol
b
Unknown
c
1.2
Nov. 23, 1994
3020
1729
387
904
2.0
Dec. 8, 1994
3142
1750
450
942
3.0
Feb. 1, 1995
3512
1871
524
1117
4.0
Jun. 6, 1995
4046
1951
667
1428
4.1
Jul. 7, 1995
4305
2012
729
1564
REFERENCES