Description:

Reading the statistical model to predict both signals and exons (scoring functions) and the gene model rules which allowed connections between exons according to their type and the distance between. Data is input from a separate file (parameter file) to an array of isochore data structure.

Briefing:

void readLine(FILE *File, char* line)

Read one line of numerical values (maximum MAXLINE characters). Skip comment lines (begin by '#') and empty lines.

void readHeader(FILE *File, char* line)

Read one line (name of some parameter) (maximum MAXLINE characters). Skip comment lines (begin by '#') and empty lines. Headers are textual labels, so user may modify them without being verified the changes.

void ReadProfile(FILE *RootFile, profile* p, char* signal)

Acquire statistics about signal prediction: definition of the position weight array (length, offset, cutoff and Markov chain order profile) and transition probabilities.

void ReadIsochore(FILE *RootFile, gparam* gp)

Read and save the information about signal/exon prediction in an specific isochore (DNA region with a well-defined and biased G+C content): C+G min/max percentages cutoff score for every type of exon coding potential score for every type of exon weight of coding potential score against signal score in the total score for every type of exon (from 0 to 1) exon weight parameter (correct the length of predicted genes) for every type of exon profiles (PWAs) to discover splicing and translation signals information about Markov chains measuring the coding potential property in predicted exons (biased distribution of some oligonucleotides in protein coding DNA) (Initial and transition matrices). Max number of donors per acceptor (building exons).

int readparam (char *name, gparam** isochores)

Main routine for the management of reading parameter file: identifying the source (command line option P, enviroment var GENEID, default) number of isochores to read loading isochores information read the gene model rules for the assembly of predicted exons

Enrique Blanco Garcia © 2001