Due to the advent of 2nd generation sequencing technologies, exhaustive multi-genome comparisons of 100s or 1000s of human genomes will soon become a reality. This will have profound benefits for personalized disease diagnostics and therapeutics.

However, the informatics challenges presented by these technologies are already creating sequence mapping, assembly and analysis bottlenecks. As reads generated from these low cost ultra-high-throughput sequencing solutions are typically 25bp to 200bp, with error rates as high as 5%, genome assembly and analysis become exponentially more complex.

Synamatix has addressed many of these issues by using SynaBASE™, which is a scalable, high-throughput database solution that leverages sequence complexity and exhaustive word-based searching to yield optimum results. SynaBASE exhaustively identifies all k-mers within biological sequences, storing the data as k-mers structured on the basis of their inter-relationships. By using a search application built on top of SynaBASE, 1.68 million 120mer reads were mapped back to the human genome in 5 hours.

In a similar experiment to handle 25mer reads, a non-heuristic search strategy employing a scoring matrix for sequence quality was used. Mapping was achieved at an average rate of over 1,000 reads/sec back to a SynaBASE of the human genome. The sensitivity and performance improvements of several magnitudes of this approach over conventional tools such as MegaBLAST validate the potential technology fit between 2nd generation sequencers and SynaBASE.

As the rate of genome sequencing continues to increase, development of methods that further enhance the efficiency of genome assembly and finishing becomes ever more critical. The advent of the so called “$1000 – (1 day) Human genome” will exacerbate this need exponentially. Synamatix has completed research and development of SynaMer which is designed to complete ultra-fast and accurate processing of sequence reads prior to large scale genome assembly. The application enables identification of all unique overlapping 96-mers within a data set. SynaMer enables a 100-fold reduction in the time taken to process a mammalian genome. There is also an improvement in the quality of the assembly as the capability to extend to longer k-mers enables gaps or repetitive regions to be linked together.

Prokaryotic evolutionary delineation has long been the subject of intense investigation and has previously been based primarily on the highly conserved ssu-rRNA. The availability of more genomic sequences has now made whole genome phylogenetics a possibility. Through the use of a structured network database of k-mers called SynaBASE™, it is proposed that phylogenetic analysis of whole prokaryotic genomes can be inferred in a fraction of the time it takes using conventional methods. SynaBASE is a novel structured network index database for indexing genomic sequences based on the location of unique k-mers. The use of such a system would be of tremendous benefit towards the elucidation of eukaryotic evolutionary phylogenetics as well as data from the advent of the "Personal Genome Project" for personalised medicines.