Why is the organism that the genomic sequence is from important?
Since the genomic sequence is the one that has the splice sites, Spidey needs to know what organism the genomic sequence is from so that it can use the correct splice site matrices. Spidey has splice site matrices for vertebrates, Drosophila, C. elegans, and plants. What do the minimum percent identity and minimum length boxes do? The minimum percent identity and mRNA length coverage are cutoffs that Spidey uses to evaluate the final alignments. If the percent identity of the final alignment is lower than the specified cutoff, or if the percent of the mRNA’s length that is covered by the alignment is lower than the percent length chosen, the final alignment will not be reported. 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
