Description:

Control of signal and exon prediction and scoring functions, both in positive and negative strand processing, in a range (l1,l2). Main parameters are the input sequence (forward or reverse), length of sequence, coordinates of the ends of the fragment, the pack of sites and exons to be filled in, scoring model (isochores) and GC information precomputed before about G+C content on that split.

Briefing:

void manager(char *Sequence, long LengthSequence, packSites* allSites, packExons* allExons, long l1, long l2, int Strand, packExternalInformation* external, packHSP* hsp, gparam* gp, gparam** isochores, int nIsochores, packGC* GCInfo)

Stablishing limits in the fragment for signal prediction (and therefore the exon construction, as well) because of the overlapping processing of fragments in which exons must be predicted following an order and repeated exons are not allowed. Search by signal: start codons, acceptor and donor splice sites and stop codons. Construction of exons: every feasible pair of left and right signals (specific depending on the exon type) will be used to build one exon as long as the parameter Max_donor_per_acceptor (maximum right signals used together with the same left signal to build different exons) in the current isochore is not reached. Scoring exons according to the G+C content in the region around every exon. Due to the pre-processing step done before (packGC), there is no need to scan the sequence for each exon. NOTE: Reverse prediction implies recomputing signal positions according to the forward sense of the original sequence (remember they have been predicted reading the reverse sequence and therefore, having reverse coordinates). Moreover, left and right signals must be exchanged to preserve the property: left signal position < right signal position.

Enrique Blanco Garcia © 2003