Signatures will appear at the bottom of this page once the
search is complete. The result of the search will be a list of
signature chains and the corresponding DNA sequence from the reference genome. A
signature chain is a set of consecutive 20-mer signature words. Intervals are
given as the start of the first signature word and the end of the last signature
word in the chain. Thus, the interval [s,e] contains exactly
e-s-20+2 signature words, completely covering the interval
[s,e] in the reference sequence.
Signature words are perfectly conserved by all target genomes, and contain at least
a single difference from every background sequence. Therefore, a signature chain will
contain a difference with the background at least every 20 bases. For some types
of detection assays, these signatures can still cross-react with background sequences
and return false positive detections. However, we have found that long signature
chains (e.g. >100bp) are often quite dissimilar from the background and make good targets
for detection assays. After identifying these candidate target sequences, we recommend
performing a more sensitive background screen of the individual signatures
using Blast to assure they are sufficiently unique.
