Microreads - Illumina
SXOligoSearch is able to handle reads longer than 32 nucleotides as well as mutation due to indels. In the recent publication on the Venter Genome, 4 million mutations were identified, of which more than 1 million were due to indels.
Gapped Alignment Distribution reported by SXOligoSearch on a set of 12,623,596 human genome Illumina sequencing reads. A plot is shown for PRB and FASTA formatted reads to highlight the difference between using quality values versus raw sequence. 7,380 (0.05%) PRB reads had unique alignments with insertions/deletions whereas 77,437 (0.61%) FASTA reads contained gapped unique alignments. Gap opening and gap extension penalties of 8 and 6 were used respectively.
Coverage of the human genome by unique read alignments increases with longer sequencing reads. 24,000 reads were randomly sampled from the human genome at variable lengths of 15-45 bp and mapped back to the reference sequence using parameters for exact matches, 1 mismatch and 2 mismatches. The number of single-match/unique alignments were enumerated. Alignment tools such as Eland are limited to 32 bp maps at most 81.4% of all possible unique alignments. SXOligoSearch maps reads without any read length limitations.

Short reads - 454
  • By using SynaSearch™ which is built on SynaBASE, 1.68 million 454 reads were mapped back to the Human Genome in 5 hours.


  • In a benchmark study, 20,000 sequences with an average length of 100bp were mapped to the Human Genome using MegaBLAST and SynaSearch. SynaSearch performed nearly 80 times faster than MegaBLAST and was more sensitive, with a query coverage of 90.2%, as compared to 77.98% with MegaBLAST.
Sanger reads - ABI

Detailed performance benchmarking was conducted to compare the analysis time taken by SynaSearch, a sequence alignment application built on SynaBASE, to BLASTz.

In comparison to BLASTz, SynaSearch:
  • was 219 times faster.
  • found 11% more true positives.
  • had 17% more unique hits to queries.
  • had a higher specificity.
  • reported 113% fewer false positives.
  • had fewer multiple placements per read.

University of California – Comparative genomics
In this case, the user needed a complete comparison of all Human and Mouse chromosomes. Using Synamatix technologies, the task took 6h 37min in contrast to BLAST which takes 3 years in terms of processor time.

Flexibility of having multiple tools on a single programmable SynaBASE platform
The programmability of SynaBASE via the SynaAPI enables the development of tools, making analysis more flexible on a single SynaBASE. The SynaAPI facilitates the development of different applications on SynaBASE, where the user can utilise multiple tools to analyse the data. In a recent case, a user requested an analysis of a specific protein group. To achieve this, a set of source protein sequences were constructed into a SynaBASE. Several tools were applied to find similar proteins with SynaSearch. Protein sequences with a defined set of patterns were extracted using SXPRESearch. The identified sequences were then subjected to SynaTree where the relationships of the proteins were inferred.

Having a single platform with multiple tools offers flexibility in analysis. At the same time, SynaAPI offers the opportunity to custom-develop applications for specific requirements. This extends the shelf-life and value of SynaBASE where users are not limited to single tool on a platform, but are open to leverage on other existing tools and develop new tools for novel requirements.