How does the program handle short exons?
GrailEXP can identify exons as short as 10 bases (although this happens when the BLAST alignment is longer than this and gets shrunk to align to splice sites). It is likely that GrailEXP could recognize short exons very well, first determining the possible presence of a short exon through detection of a “bump” in the alignment, and then through checking the donor splice site score to see if it’s good. This has simply not been done to date, however, so the current version does not recognize short exons well. It does put its alignment pieces in the proper frames, though, so missing a short exon will only cause a slight ripple in the resulting translation. GrailEXP finds short exons (as short as 5 bases) at the edges of the alignments (with the criterion that the bases in the message must exactly match the genomic sequence). This is critical for aligning CDS portions of transcripts with genomic sequence, where one may have very short exons at the edges of the gene.
