Sequence logos (Schneider & Stephens, 1990) for human donor and acceptor splice junctions (Stephens & Schneider, 1992) compared to the consensus sequence for both sites. Source: Adapted from (Stephens & Schneider, 1992).

Sequence logo for random sequences.
Error bars, shown by I beams, indicate one standard deviation of the stack height. Note that a small-sample correction (Schneider et al., 1986) suppresses the stack height so that a position such as -19, which is 50% C and 50% G, is lower than 1 bit. The correction is needed to counter a statistical bias that causes an apparent information to appear when one substitutes frequencies for probabilities in Shannon’s equation (Schneider et al., 1986; Miller, 1955; Basharin, 1959). The same effect makes one tend to see patterns where there are none. The consensus sequence on the bottom was chosen from positions that have 50% or more of one base. S is the two-letter code for C or G.

Sequence logo for RepA binding sites.
Error bars indicate standard deviations of the entire stack height. Source: Adapted from (Schneider, 2001).

Consensus versus R_sequence.
The information for the 5 sequence logos in figures 1, 3, 5, and 6 was graphed by comparing the information content (R_sequence) to the information content of the corresponding consensus sequence. R_sequence is the average information in a set of binding sites. It is also the summed area under the sequence logo. The line at 45° represents equality between the two measures. The data are summarized in Table 1.

Sequence walkers (Schneider, 1997b) for a human acceptor site in the iduronidase synthetase gene and a mutation (indicated by an arrow). On the top sequence, the normal end of exon 4 is shown by a bracket and dashed line. The vertical rectangle on a sequence walker is the ‘zero base’ used to identify the location of the walker. The vertical rectangles also indicate a scale from -3 to +2 bits. A 12.7 bit acceptor at 5154 directs splicing to the correct location. Source: Adapted from (Rogan et al., 1998).

Region upstream of the tgt/sec promoter of E. coli analyzed by Fis sequence walkers. The information for each Fis site was computed from models that are 21 bases wide (-10 to +10) but only the range -7 to +7 is shown by walkers. The sine waves represent major (peaks) and minor (valley) grooves faced by the Fis protein. Source: Adapted from (Schneider, 1997b).

Sequence logo for the -10 region of E. coli promoters.
The promoters were from the Lisser-Margalit database (Lisser & Margalit, 1993). The dashed and solid boxes show the regions opened by the polymerase, while the arrow shows the start points of transcription. Source: Adapted from (Schneider, 2001).