Perceval reads in a DNA sequence and produces a list of possible Grail Exon Candidates. It also filters these candidates against a repetitive element database. It also locates repetitive elements and CpG islands. A Grail Exon Candidate is a region identified by the Grail neural network as being a potential exon.
Candidates have a begin, end, strand, and frame.
They begin with either a start codon or AG acceptor splice site and end with either a stop codon or donor splice site. The candidates are subdivided into clusters, with the highest scoring exon in each cluster clearly indicated. All possible candidates within a sequence are then examined. For each candidate, coding scores are calculated. These scores, along with the splice site scores and GC content information, are fed to the final neural net, which produces a final score for that exon.