When is the Properties Information Useful?

4.3.1

The multi-alignment of the Global and Consensus Align tabs display only the non-Primer portions of the aligned reads. In certain situations, however, it may be useful to be able to examine the sequences flanking the aligned sequences (or indeed, the whole original sequencing read). For example, if a read appears to be aligned so poorly that you think it might be a contaminant, it might be useful to examine the part of the read that was considered as a Primer match by the alignment software, to determine if some mispriming might have occurred. Conversely, if a read appears to terminate too early in the alignment, one might want to check if the sequence is really that short, or if it was truncated by some unforeseen problem with the aligner, or if it was due to sequence quality issues. Or, if a read exhibits a large deletion at the edge of an alignment, it would be useful to see the sequence from the read beyond the edge of the alignment, to determine if there is a significant match that supports the deletion or if the aligner arbitrarily placed some trailing bases far from the adjacent bases of the read when they actually could have been aligned closer.

The “properties” window of a Consensus or a read provides the necessary information for such verifications, e.g. the full original sequence read, as well as the aligned and flanking sub-regions of the read (see details below, section 4.3.2). These are all provided in FASTA format, which can be copied to the clipboard and used in external search or analysis programs. In particular, one could BLAST a sequence to determine its identity if it is either aligned so poorly that it looks like a contaminant; or if it has such specific variation compared to the Reference Sequence that it looks like it might be a homolog or a paralog of the intended Amplicon rather than a regular Variant of the Amplicon. One can also compare a sequence to dbSNP to see if a particular Variant has already been identified in the literature.