Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms - PubMed (original) (raw)

. 2004 Jan 1;32(Database issue):D311-4.

doi: 10.1093/nar/gkh033.

Shuai Weng, Rama Balakrishnan, Maria C Costanzo, Kara Dolinski, Selina S Dwight, Stacia R Engel, Becket Feierbach, Dianna G Fisk, Jodi E Hirschman, Eurie L Hong, Laurie Issel-Tarver, Robert Nash, Anand Sethuraman, Barry Starr, Chandra L Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, J Michael Cherry

Affiliations

Karen R Christie et al. Nucleic Acids Res. 2004.

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new resources that allow the comparison and integration of information on a genome-wide scale, enabling the user not only to find detailed information about individual genes, but also to make connections across groups of genes with common features and across different species. The Fungal Alignment Viewer displays alignments of sequences from multiple fungal genomes, while the Sequence Similarity Query tool displays PSI-BLAST alignments of each S.cerevisiae protein with similar proteins from any species whose sequences are contained in the non-redundant (nr) protein data set at NCBI. The Yeast Biochemical Pathways tool integrates groups of genes by their common roles in metabolism and displays the metabolic pathways in a graphical form. Finally, the Find Chromosomal Features search interface provides a versatile tool for querying multiple types of information in SGD.

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Figures

Figure 1

Figure 1

The Fungal Alignment Viewer. The Fungal Alignment Viewer displays available fungal sequences related to an S.cerevisiae sequence of interest. At the top of the display is a dendrogram showing the relationships between all included sequences. The available sequences are aligned via ClustalW with color coding to indicate conservation (yellow = identical, pink = strong similarity, green = weak similarity). Above the ClustalW alignment is a control menu that allows selection of sequences and type of alignment (protein, ORF DNA, upstream sequence, downstream sequence, ORF DNA + 1 kb up/downstream). When the ‘Align’ button is pressed, the alignment is recomputed according to the user’s selections. Individual sequences present in the alignment are displayed below the ClustalW alignment (not shown here). In the alignment shown, the partial sequence from S.mikatae, available from the sequence selection menu, has not been included so that sequence similarity between the C-terminal portions of the other available sequences can be visualized by ClustalW.

Figure 2

Figure 2

The Sequence Similarity Query Tool. In the graphical summary of the Sequence Similarity Query tool, a dendrogram shows the relationships between the sequences in a protein family. A bar graph shows the distribution of members of the protein family within broad taxonomic groupings. The color coding used in the bar graph is also used for the names of the sequences within the dendrogram to indicate the taxonomic grouping.

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