Expanding yeast knowledge online

Abstract

The completion of the Saccharomyces cerevisiae genome sequencing project and the continued development of improved technology for large-scale genome analysis have led to tremendous growth in the amount of new yeast genetics and molecular biology data. Efficient organization, presentation, and dissemination of this information are essential if researchers are to exploit this knowledge. In addition, the development of tools that provide efficient analysis of this information and link it with pertinent information from other systems is becoming increasingly important at a time when the complete genome sequences of other organisms are becoming available. The aim of this review is to familiarize biologists with the type of data resources currently available on the World Wide Web (WWW).

Figure 1

The Gene/Sequence Resources information retrieval Page at SGD. After searching by gene name (here, ACT1) at the Gene/Sequence Resources search form (http://genome–www2.stanford.edu/cgi–bin/SGD/seqTools), the results are displayed as shown. Each of the categories is linked to the relevant ACT1 site. For instance, if the user clicks on BLAST Search under Sequence Analysis, the BLAST form is displayed, already containing the ACT1 sequence.

Figure 2

The SAGE tag viewer at SGD. After searching for ACT1 at the Query SAGE data page (http://genome–www.stanford.edu/cgi–bin/SGD/SAGE/querySAGE), this SAGE map is displayed. By clicking on the SAGE sequence tag on the graphic display of the chromosome, the user can retrieve detailed information about that particular SAGE sequence tag, including its sequence and expression results. Links at the bottom of the page (Genomic View, Gene/Sequence Resources) provide access to other information about the chromosomal region.

Figure 3

Alignment of the yeast centromeres at MIPS. This multiple sequence alignment of all the yeast centromeres was created with PILEUP. Each centromere name is linked to the MIPS page containing detailed information about it. In addition, there is a link at the bottom of the page to literature characterizing the centromeres.

Figure 4

Cellular localization of YTA proteins at MIPS. Each yeast protein name is linked to the MIPS page describing the characteristics of the protein and the gene encoding it.

Figure 5

Long search form at YPD (http://www.proteome.com/search1.html). The user can search for sets of proteins that belong to several categories; the subcellular localization parameters are shown here.

Figure 6

Protein report at YPD. After searching for the gene name CTT1 with the YPD short search form (http://www.proteome.com/search0.html), the Protein Report is displayed; shown here is the first page. By scrolling down, the user can view an extensive summary of the literature, which contain links to the PubMed abstracts.

Figure 7

TCA cycle at Kyoto Encyclopedia of Genes and Genomes. Each label in this metabolic pathway is linked to more information. For instance, clicking on the Aspartate metabolism label will send the user to the diagram of the Aspartate pathway. Enzyme numbers are linked to pages containsing more information about that particlular enzyme, including links of sequence retrieveal.