SynaHybridise™ is an ungapped, non-heuristic oligonucleotide
sequence verification tool, designed to validate microarray probe
specificity and uniqueness.
Ungapped, non-heuristical weight matrix search offers improved
sensitivity in finding targets with multiple mismatches within a short
oligonucleotide sequence. Linear weighted search penalizes all
mismatches equally, while centre weighted uses lower penalties for
mismatches near the probe ends than for mismatches near the centre.
Centre weighted searches are designed to be consistent with reports and
observations that indicate sequences with mismatches near the end of a
probe may still hybridise and produce a false positive signal. Common
heuristical search tools using fixed k-mer seeds to search for
sequences that potentially bind to microarray probes have low
sensitivity and specificity. Therefore by using SynaHybridise, centre
weighted search provides a faster and more accurate method for
validation of microarray probes.
A sample 25mer probe (Figure 1) is used with linear weighted and centre
weighted searches against a SynaBASE of
the full Human genome. The result of the linear weighted search (Figure
2) shows a contrast to the centre weighted search (Figure 3), in which
there are more targets with mismatches biased towards the ends of the
probe. Results of searches with BLASTN (Figure 4) and BLAT (Figure 5),
using fixed k-mer seeds miss targets found by SynaHybridise. In terms
of performance, both BLASTN and BLAT would require a cluster, while
SynaHybridise runs on a single server to return the result within
seconds. This clearly demonstrates the advantage of using an ungapped,
non-heuristic weight matrix search approach as an improved alternative
to verify the specificity and uniqueness of microarray probes.
try SynaHybridize, please:
- Click here and then click on the
“Access Now” button.
- Click “Test Sequence”
(written in grey on the left hand side)
- Click ‘Copy’ to
select the newsbyte test sequence.
- Select the ‘Linear
Weighted’ search option and set ‘Maximum
Mismatches’ to 4. Click ‘HYBRIDISE’ to
begin your analysis.
- Go back to the query page, and now select
the “Centre Weighted” search option and set the
“End letter mismatch score” to -0.4, and set
“Threshold” to -4. Click
‘HYBRIDISE’ to begin your analysis.
Figure 1: Input page with the sample
probe and parameters.
Figure 2: Linear weighted search finds
targets with mismatches at equal penalty settings.
Figure 3: Centre weighted search finds
targets with mismatches biased towards the ends of the probe.
Figure 4: BLASTN searches are restricted
by word size (word size 7, e-value 1000), and miss other potential
cross talk targets that SynaHybridise identified.
Figure 5: BLAT only reports one exact