ReadSR.c geneid v 1.1 source documentation


Description:
Similarity regions (SRs) are projections of blast High-scoring Segment Pairs over the input sequence (saving for every basepair the score of the better HSP), depending on the frame. By using these homologous regions to the input DNA sequence, exons overlapping the SRs will be enhancered and better predictions will be obtained.

  • SRs file is in gff format (8 mandatory records plus string group optional).
  • SRs file need not to be ordered by any field.
  • If blastn (DNA vs DNA) is used to obtain the homologous regions, their frame is unknown, so a dot (".") must be used to make three copies from every one.
  • HSPs from blast may be used instead project them into SRs but then, predictions quality might decrease due to the number of HSPs is usually much more bigger than the amount of SRs computed from them.
Briefing:
long ReadSR (char* FileName,
             packSR* sr,
             long LengthSequence)
To place every SR 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 SR will be produced. (It is not necessary a previous sorting in the SR file)




Enrique Blanco Garcia © 2001