Figure 1.
A typical motif alignment from GLAM2.
The stars indicate the key positions. The residues inserted between key positions are not considered aligned to each other: their column placement is arbitrary. The numbers on either side of the aligned segments indicate the coordinates of each segment within the sequence. The decimal numbers on the right are the marginal scores of each aligned segment.
Table 1.
Comparison of GLAM2 with sam-t2k and pratt on 58 PROSITE motifs.
Figure 2.
Sensitivity and positive predictive value of GLAM2 compared to sam-t2k and pratt on 58 PROSITE motifs.
Figure 3.
Non-specificity of ELM motif regular expressions.
Each point represents one of the 41 ELM motifs used in this study. The x-value of the point is the number of known sites, and y gives the number of predicted sites in Swiss-Prot sequences.
Figure 4.
Sensitivity versus specificity trade-off of GLAM2 motifs.
(A) shows how often the glam2 motif has better specificity than the corresponding ELM RE as a function of the sensitivity level. (B) shows the specificity (FP_50) of the ELM RE and the glam2 motif for each of the 41 ELM entries studied here. Each point represents one ELM motif, with x and y giving the the FP_50 of the glam2 motif and of the ELM RE, respectively. Triangles are motifs learned from all sites; squares show cross-validated results.
Table 2.
ELM families where GLAM2 motifs are massively more specific.
Table 3.
Average GLAM2 performance on each BAliBASE category.
Table 4.
GLAM2 motifs in protein kinase substrates.
Figure 5.
GLAM2 output on 31 clones that bind the Lmo2 complex.
glam2 was run using default parameters on the clones identified in Figure 1A of [46]. The glam2 alignment is shown on the top, and the information content “LOGO” corresponding to the alignment is shown on the bottom. The glam2 alignment was pretty-printed using PFAAT [60]. The LOGO is corrected for small-sample size [61].