JaMBW Chapter 4

Genetical and functional site mapping

Whever sequences of DNA or PROTEINS or RNA are available, a commonest question that is posed is to identify which functions are encoded by the Macromolecular information system which we have just discovered. This extremely valuable question is unfortunately not so straightforward to answer, mostly since the knowledge on the correlation between sequence/structure and function is still limited.

Typical approach in order to investigate on the potential functions of a sequence is to observe which features does it show that already had been identified in other well-studied molecules. This approach is called "pattern matching" and its implementation offer to the Computer Science and to the Computing resources a mathematically challenging problem. The applets hereafter wants to offer the best solution to the problem, and although still in their infancy are capable of answering basic questions of this sort. Usually such patterns are identified as "motifs" and consist of difficult to spell combinations of words and symbols (e.g. )

Another reason for doing genetical and functional site mapping is in the design of new sub-cloning experiments, whereas the problem is to identify "where to cut" and "what can be cut". This is called Restriction analysis and coincide with the above mentioned pattern analysis. The only difference being usually a very short pattern.

  1. find patterns / binding / restriction sites in DNA and PROTEINS (Luca Toldo)