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September 15, 2007 (Vol. 27, No. 16)

Regulatory Sequence Analysis Tools (RSAT)

  • Much useful information
  • Poor organization
Hosted at Brussels University, RSAT tackles the challenging but important problem of identifying sequence elements involved in genetic regulation. As most scientists know, expression of proteins is a complex phenomenon controlled ultimately in eukaryotes by the binding of specific proteins (transcription factors) to specific sequences in the genome. The effects of binding may be positive or negative, causing transcription to be either activated or repressed respectively. One approach is to isolate a transcription factor and then assay which sequence(s) in a DNA it binds to. Isolating transcriptional factors is not trivial, so computational analysis for identifying such sequences is an important tool. The approach of the site is simple in principle—compare a set of noncoding regions near genes to random sequences and flag those which stand out. Then, by comparing to known regulatory sequence motifs, identify final candidate sequences. It sounds great in theory. I’ll be interested to learn of reader’s successes using the resource.
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