Figure 3

A summary of the psb A sequence classifier. Each sequence is classified by two independent approaches: multi-class SVM (left) and cuPSSM (right). In the multi-class SVM classifier, each sequence is represented by an oligonucleotide frequency vector (calculated in overlapping windows) and tested against seven different SVM classifiers (trained on culture and environmental data from GOS) [See Additional Files 1 and 2]. The sequence is classified based on the classifier in which it achieved the highest positive result. Independently, the sequence is aligned to a template psb A gene and scored against seven different cuPSSMs. The sequence is then classified based on the subgroup for which it achieved the highest score. Finally, the results of the two approaches are compared. Sequences for which the two independent classifiers converged are classified according to the common sub classification. In cases where no agreement exists, the sequence is further classified manually as described in the text.