How is Spidey different from Blast2Sequences?
Spidey is specialized for doing spliced alignments. After an initial BLAST search, Spidey sorts through the hits to find a set of alignments that are consistent and that cover the mRNA pretty well. Then, Spidey tries its hardest to align any pieces of the mRNA that aren’t yet aligned — to do this, it uses low-stringency BLAST as well as another type of local alignment program. Finally, Spidey uses splice matrices to adjust the boundaries of the exon alignments so that they do not overlap or underlap and so that they are adjacent to good splice sites. Does Spidey look at annotation in Genbank to help arrive at a gene model? Short answer: no. Longer answer: The strength of the evidence for intron and exon features annotated in Genbank varies widely. Since many of these have been found by programs, not through experimental work, it doesn’t make sense to use these annotations because then Spidey would just pick up all the quirks of other alignment programs. Also, since Spidey was designed
