Analysis of SELEX Experiments

Different aptamers from a SELEX experiment (see chapter 7) often evolve the same secondary structure to perform their function. However, it is often not possible to obtain good sequence alignment, and thus RNAalifold (or similar programs based on a sequence alignment) cannot be used to find the conserved structure. 

In principle, the Sankoff algorithm [7] can compute a consensus structure and an alignment simultaneously, but it is rarely used, due to its high computational cost. You can try foldalign [1], a simplified version of the algorithm that excludes multiloops. It is available as a web service at http / /www. bioinf. au.dk/ FOLDALIGN/. 

Of course, you can also predict and compare individual structures. 

Do a cluster analysis to find sequences with similar structure  

Another alternative is to compute an alignment of the predicted MFE structures. The RNAf or ester program is a new tool to perform such structure alignments and can also construct multiple alignments (in contrast to KNAdistance above). It is available as a web service at http / /bibiserv. techfak. uni-bielefeld.de/rna-forester/ although it does not yet offer multiple alignments. 

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