8.5 years ago by
Maastricht, The Netherlands
Ha, this could become really philosophical.... Or it already is considering David's comment.
But let us do the basics first. In bioinformatics we use the word sequence for a series of chained biomolecules, either a sequence of nucleotides (making up dna and rna) or a sequence of aminoacids (making up a protein). In both cases we use letters to indicate individual bases or aminoacids. And since we are sometimes not sure about bases we use other letters to indicate ambiguity, up to an "X" where it can be anything. We normally (somebody will probably come up with an exception here...) do not use dashes to indicate sequence components. We use the dashes in alignments of two sequences, to indicate there is something missing in one of them that is present in the other. A dash indicates a gap. but that is not a physical gap! The sequence really is connected. The gap is only part a comparison. So the enlightened one might say something like "a dash is something that is absent in my mind, but nothing is missing in reality".
So to answer your question. No, I would not consider a series of dashes a sequence. But if what you want to do is parsing sequence comparisons I would certainly take them into account.