Figure 1.
Visualization of Protein Sequence Similarities
Sample from a Web page used by annotators of the C. albicans genome to visualize the significance of the best hit from whole-proteome BLASTP searches. Each putative ORF was compared to the NR database, the Candida ORF list itself (Ca19; showing results from the four top hits), and amino acid sequences from the proteomes of S. cerevisiae (Sac), S. pombe (S.p), M. grisea (Mag), N. crassa (Neu), H. sapiens (H.S), M. musculus (M.m), D. melanogaster (Dro), C. elegans (C.e), and A. thaliana (A.t). The BLASTP e-value from the top hit was converted to a color scale as indicated. Examples of C. albicans genes with interesting similarity patterns are indicated.
Table 1.
Features of Completed Fungal Genomes
Table 2.
Statistics of the C. albicans Annotation
Table 3.
Number, Abundance Ranking, and Proportion of Gene Products Containing the Indicated Interpro Protein Domain in C. albicans and Other Eukaryotes
Table 4.
Genes from C. albicans with a Strong Homolog in the S. cerevisiae, S. pombe, A. niger, M. grisea, and N. crassa genomes but Absent from the H. sapiens and M. musculus Genomes
Table 4.
Continued
Table 4.
Continued
Table 4.
Continued
Table 5.
Frequency and Characteristics of Short Tandem Repeats in the Coding Sequences of Fungal Genomes
Table 5.
Continued
Figure 2.
Identification of Spurious Genes
Assessing criteria that identify candidate spurious genes in S. cerevisiae, using a reference set of known spurious genes [16].
(A) For every gene in S. cerevisiae, the average Pearson correlation coefficient with all other genes was calculated. Shown are histograms of the correlations associated with genes characterized as spurious in the reading frame conservation test ([16]; red) and all genes in the genome (black).
(B) The distribution of gene lengths is shown for genes characterized as spurious (red) and for all genes of the genome (black).
(C) Assessing the likelihood of being spurious as a function of gene length and correlation score. Shown is the proportion of spurious genes out of all genes whose length and correlation score fall into each of the intervals. The proportion is color-coded according to the color bar shown. S. cerevisiae genes with an ortholog in C. albicans were excluded from the analysis.
Table 6.
Genes Encoding Members of the ABC Transporter Family
Table 7.
Assembly 19 ORFs That Correspond to ALS Genes
Table 8.
Phospholipases in C. albicans