geneid.c geneid v 1.2 source documentation

Main program: management and control of geneid data flow.
void main (int argc, char *argv[])
geneid main program actions:
  • Initialize accounting structure
  • Read setup options from command line
  • Set ratios (for sites/exons memory allocation) from file size estimation
  • Request memory for main geneid data structures
  • Read parameters file (statistical model to predict genomic elements)
  • [optional]. Read annotations and homology SRs from input file
  • Read first DNA sequence from input file (more than one allowed)
  • Processing sequence: upper case, reverse and complement
  • Divide sequence into overlapped fragments (length = LENGTHSi)
  • For every fragment do:
    • Measure G+C content to select the proper isochore
    • Forward strand predictions: sites, exons (both scored and filtered)
    • Reverse strand predictions: sites, exons (both scored and filtered)
    • Merge forward and reverse predicted exons (and annotations)
    • Integrate external information: evidence and HSPs
    • Sort by left (minor) position the whole set of predicted exons
    • Print genomic elements: sites and exons (selected format)
    • Run genamic algorithm to assemble the best gene possible
    • Save necessary information to go on computing the next fragment
    • Delete the rest of information (to save memory)
  • Print best prediction: multiple gene output (selected format)

There is a partial prediction mode: reading exons directly from input file and running assembling algorithm (genamic) to display the best gene predicted

Enrique Blanco Garcia © 2003