ReadHSP.c geneid v 1.2 source documentation


Description:
Read the external file containing HSPs from sequence alignments. Blast High-scoring Segment Pairs over the input sequence are projected over the input sequence, taking the best value in every position. Positions without homology support are assigned the value NO_SCORE (parameter file). By using these homologous regions to the input DNA sequence, exons overlapping any HSP will be enhancered and better predictions will be obtained.
  • HSPs file is in gff format (8 mandatory records plus string group optional).
  • If blastn (DNA vs DNA) is used to obtain the homologous regions, their frame is unknown, so a dot (".") can be used to make three copies from every one.
-- It is NOT necessary to provide the HSPs records ordered by any position --
Briefing:
packHSP* SelectHSP(packExternalInformation* external,
                   char* Locus,
                   long LengthSequence)
Select the group of HSPs to be integrated into the predictions according to current Locus name (using a hash table - dictionary of locus). Both FWD and RVS HSPs will be sorted using a quicksort routine.
long ReadHSP (char* FileName, 
              packExternalInformation* external)
To place every HSP into the correct array according to their blast frame (1,2,3) and strand. If frame is unknown (blastn), then 3 copies of the same HSP will be produced. (It IS necessary a previous sorting in the HSP file)




Enrique Blanco Garcia © 2003