Quantifying optimal accuracy of local primary sequence bioinformatics methods*

Traditional bioinformatics methods scan primary sequences for local patterns. It is important to assess how accurate local primary sequence methods can be. We study the problem of donor pre-mRNA splice site recognition, where the sequence overlaps between real and decoy data sets can be quantified, exposing the intrinsic limitations of the performance of local primary sequence methods. We assess the accuracy of local primary sequence methods generally by studying how they scale with dataset size and demonstrate that our new Primary Sequence Ranking methods have superior performance. Our Primary Sequence Ranking analysis tools are available at {tt http://rna.williams.edu/}