Description: SynaSearch™ is an application for rapid database searching and alignment of sequence data within SynaBASE. It harnesses the exhaustive dynamic k-mer pattern structure of SynaBASE to effectively align sequences rapidly and accurately.
Application Example: Cross referencing clinical patient sequence data back to the human genome is a necessary step for identifying potential disease states amongst different individuals. SynaSearch was able to re-map 1.68 million 120mer reads at 6x coverage from human chromosome 22 patient’s data back to the human genome in approximately 5 hours using command-line version. This approximates to being 123-fold faster than BLAST as seen in Figure 1. The examples here are a subset of the reads showing their positions on chromosome 22. We simulated point mutations at various positions in the reads and correct placement of these reads to the human genome (NCBI version 36) shows the sensitivity of our alignments. The applicability of this tool could also be translated to rapidly map Solexa-based sequencing reads or a combination of both.
Figure 1:  Performance comparison of mapping 1.68 million 454-type patient reads back to the human genome (NCBI36).

To try SynaSearch, please:

1. Click here and then click on the “Access Now” button
2. Click on “SynaSearch”.
3. Clear the ‘Query Sequence’ box and copy the sequence below into the box.
4. Select the ‘Homo Sapiens Genome (NCBI Build 36 v1)’
5. Using the default parameters, click on ‘Search’ to begin your analysis.
Read 1:
The top alignment to chromosome 22:
Test Sequence for this Newsbyte: