Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is a scientific database of gene, protein and genomic information for the yeast Saccharomyces cerevisiae. SGD has recently developed two new resources that facilitate nucleotide and protein sequence comparisons between S.cerevisiae and other organisms. The Fungal BLAST tool provides directed searches against all fungal nucleotide and protein sequences available from GenBank, divided into categories according to organism, status of completeness and annotation, and source. The Model Organism BLASTP Best Hits resource displays, for each S.cerevisiae protein, the single most similar protein from several model organisms and presents links to the database pages of those proteins, facilitating access to curated information about potential orthologs of yeast proteins.

Figure 1

Summary table of the Model Organism BLASTP Best Hits page. A summary table similar to this representative table is generated for each locus having a ‘hit’ in one or more model organism databases. In this figure, Saccharomyces protein Yer179wp results are shown as an example. Columns of the table are as follows: species of the hit protein; name of the database for the hit protein, hyperlinked to the home page of that database; name of the hit protein from its database, hyperlinked to the database page of that protein or its gene; description of the hit protein, as found in its database; E-value (expectation value), reflecting the number of hits expected to be found by chance; percent aligned, showing the percentage of the length of the query protein over which it aligns with the hit protein; source range, showing the amino acid coordinates of the region of the S.cerevisiae query protein that was aligned; and target range, showing the amino acid coordinates of the region of the ‘hit’ protein that was aligned with the S.cerevisiae query protein.