What are the disadvantages of using Blast?
BLAST doesn’t look for short pieces. This means any short exon finding must be done by GrailEXP’s alignment program. As such, the program is weak at finding internal short exons, although hopefully this will be remedied in future versions. BLAST does simple repeat filtering that causes it to break good alignments. This is an amazingly nonsensical “feature”, as fairly simple algorithms can tell when the pieces should be put back together. An example is that BLAST will align bases 1 to 100 with bases 1 to 100 of a reference, and bases 201 to 300 with bases 201 to 300 of a sequence, all with 100% identity. But bases 101 to 200 will be left out if they are a simple repeat, even if they are 100% identical. One can run BLAST with simple repeat filtering turned off, but this results in an inordinate amount of noise. Ideally, BLAST should filter for simple repeats initially, but then “de-filter” to join fragments together that it incorrectly split. GrailEXP handles these cases, but the maximum
