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 to take FASTA sequences as input, it has to be able to align sequences blindly anyway. What does the moltype warning mean? If you input two accessions or gis, the sequences are retrieved from Genbank, and their annotations can be examined. Spidey looks to see whether both sequences are annotated as the same sequence type, for example, both genomic or mRNA sequences. Since Spidey is designed for mRNA-to-genomic alignments, it may give strange-looking output for genomic-to-genomic alignments or for alignments of other combinations of molecule types. The warning simply indicates to the user that he or she is trying to do somet
