Bioinformatics World is one of those sites that collects links to bioinfo-software. But it's far from listing just links. There's comments everywhere, a lot of practical experience for many programs and an extensive FAQ on how to combine some of them to solve typical problems. The tutorials from the FAQ are often better than the manuals that come with many of the bioinformatics tools, with some kind of preference for transcriptional regulation/promotor analysis, though.

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http://homepage.univie.ac.at/herbert.mayer/