The motto of Wolfram|Alpha is Making the world’s knowledge computable. Basically, it is like Mathematica plus a growing corpus of factual numeric data, plus a system to interpret user’s input. This is a nice online reference and computation platform.

CLANS runs (PSI)BLAST on your sequences, all vs all, and clusters them in 2D or 3D according to their similarity. This method allows for rapid classification of huge datasets and has the advantage over, lets say, phylogenetic tree, that one can quickly assess results of the clustering in a visual way (I cannot imagine making any sense of looking at phylogenetic tree with 1500 branches, while the graphical output, as on the animation below, is pretty easy to read).

If you are interested – have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row – see e.g. the most recent Eukaryotic transcription factor binding sites – modelling and integrative search methods.

Finally, just a useful resource if you need a shiny name for your brand-new 2.0-beta project: anagram server.