The State Model That Uses Open Reading Frame Information

<p>The sequences next to the state indicate which consensus has to appear at the transitions between intron (capital) and exon (bold). Here, we use the IUPAC code for ambiguous nucleotides (e.g., B = C/G/T, R = A/G, Y = C/T). The digit on the transition arrows is related to the reading frame and indicates the required frame shift to follow the transition (e.g., between state 1 and 2, one can only accept exons leading to a frame shift of 0). Also, it defines in which frame stop codons are allowed to occur—no stop codon should appear in-frame. Finally, the model is constructed such that in-frame stop codons cannot be assembled on the exon boundaries (this required the three additional state pairs 6/7, 10/11, and 12/13).</p

POIMs for Donor (Left) and Acceptor (Right) SVM Classifiers

<p>Shown are the color-coded importance scores of substring lengths for positions around the splice sites. Near the splice site, many important oligomers are identified. Particularly long substrings are important upstream of the donor and downstream of the acceptor site. See the main text for discussion.</p