On-the-fly analysis tools
On-the-fly analysis tools were implemented for sequences retrieved from TRED or imported from other resources (Figure 2). They currently include simple sequence manipulation and analysis tools for users' convenience and motif-matching programs based on regular expression and PWM. A word counting-based motif searching tool DWE (15) and PromoterWise, a program specifically for pair-wise promoter local alignment (E. Birney, unpublished), are also implemented. Promoters on various TRED sub-pages can be directly sent to these analysis tools at a click of a button.
In addition to the on-the-fly tools, TRED also provides links to many other sequence analysis and motif-finding programs such as MEME (16) and Gibbs sampler (17).