Synamatix Announces Release of Bioinformatics Solutions for Second Generation Sequencers

Synamatix has recently released two new software applications designed to process and analyse data from re-sequencing projects conducted with second generation DNA sequencing platforms. The huge volumes of data coupled with higher error rates and shorter read lengths is stretching conventional approaches for read mapping and differential analysis towards breaking point.

The first application, SXOligoSearch™ is designed for mapping of micro-reads (25-50bp) whereas a new version of SynaSearch™ has been optimised for reads generated from pyro-sequencing platforms such as the FLX from 454 Life Sciences.

These new applications were developed as part of an ongoing strategy to complete a suite of high-throughput applications to process, analyse and integrate data from every type of second generation DNA sequencer.


SXOligoSearch is designed specifically for genome and transcriptome re-sequencing projects that use data from second generation sequencers. By using SynaBASE™ as the underlying database platform, this tool can rapidly and accurately map micro-reads. The search process is non-heuristic and reports all alignments that fit the scoring criteria and other limits defined in the parameter settings. SXOligoSearch accepts FASTA and Solexa Bustard file formats as input, and produces pair-wise alignments as output.

Unlike the native applications, SXOligoSearch offers a very high degree of flexibility in terms of handling a wide variety of read errors or mutations. It is able to handle low-quality reads containing any number of mismatches, insertions or deletions with high accuracy and superior performance.


SynaSearch Bulk is a command line version of the web-based SynaSearch sequence alignment and search tool that is specifically designed to leverage pattern information in SynaBASE. This application is analogous to NCBI-BLAST and BLAT but it utilizes the SynaBASE structured network database as the underlying database platform.

In a recent benchmarking study 20,000 sequences with an average length of 100bp were mapped against the Human Genome using MegaBLAST and SynaSearch. The results showed that SynaSearch performed nearly 80 times faster than MegaBLAST (Figure 1) and was more sensitive, with a 90.2% query coverage, compared to 77.98% achieved with MegaBLAST (Figure 2).

Figure 1: Execution time of the tools to map 20,000 sequences against Human Genome v36.1. Figure 2: Percentage Coverage of Queries

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