Life scientists are constantly dealing with the explosive growth of genomics and proteomics data and the need for ever-more sophisticated analysis of this data.
The typical solution is to throw processing power at any problem that comes up. Yet, as the amount of data increases, the time needed to manage the data and run calculations often limits the research that can be performed.
The Malaysia-based company Synamatix is offering a different approach that relies on what it calls an intelligent structured database. The company’s name hints at what is different about its database: “Synamatix” is based on “syntax” and “semantics.”
“We’re trying to define the language of biology, constructing databases based on patterns,” says Arif Anwar, Synamatix’s vice president of commercial development.
To that end, Synamatix’s approach is to find patterns in sequence data and identify relationships between the patterns. This information is used to infer the function and significance of various patterns. All of this information – the patterns, relationships between patterns, and their significance – is stored in the company’s SynaBASE intelligent database.
Essentially, SynaBASE automatically learns and identifies similar patterns from raw data sets and stores each unique pattern only once. This helps deal with scaling (less data needs to be stored) and computational speed.
Working hand-in-hand with the SynaBASE database is the SynaSuite toolkit, which contains a number of applications developed to interrogate pattern information within SynaBASE.
For example, one tool, called SynaMine, mines all patterns in a sequence against data stored in a SynaBASE database for pattern frequency and significance.
Other applications in the toolkit include:
· SynaCompare, an application that allows for comparisons between a query sequence and an organism, chromosomes, or whole genomes stored in SynaBASE.
· SynaProbe, an application that identifies specific probes suitable for the design of whole genome microarrays.
· SynaMap, an application for mapping transcript data to genome sequences stored in SynaBASE.
All told, there are about a dozen applications within SynaSuite (most of the applications are available now; a number are yet to be developed). And all applications within SynaSuite typically run on a single computer such as a Linux system with an Itanium CPU.
Most of the applications are useful in a wide range of genomic and proteomic research efforts. To that end, Synamatix says that its tools are used in large high-throughput sequencing labs and organizations.
Additionally, some of the SynaSuite tools are intended for specific applications. For instance, FragBASE is an ultra-fast sequence assembly application that is optimized for companies and organizations in pursuit of the $1,000 genome.
Practical Issues
To demonstrate the ways SynaBASE can or might be used, Synamatix has developed a series of application notes that give detailed examples of its software applied to a wide array of life science problems. (The application notes are available on the company’s website.)
Application examples include comparison of a human and mouse chromosome, a search for finding homologies in sequences (particularly those that have undergone circular permutations), and a search of HIV variants against a single HIV virus.
The application notes are designed to give potential users of the Synamatix software some idea of the performance they can expect for certain classes of analysis.
To get its software to end-users, Synamatix has used a direct-to-the-end-user approach. The company has users throughout the world, and it hopes to beef up its U.S. presence with the opening of an office here this year.
Additionally, last year the company, through its affiliate the Malaysian Genomics Resource Centre (MGRC), started offering its applications on a pay-per-use basis. It also has a free application, SynaBLAST, which is a BLAST equivalent running on SynaBASE. Specifically, the MGRC is an online service provider platform for high-throughput sequence analysis tools. According to Synamatix, the effort has been branded the “My Genomics Research Centre” to reflect that the services are intended for individual researchers.
Related Stories:
ChemAxon Offers Cheminformatics Toolkit for Public Databases
Tripos Signs Deal With Wyeth Pharmaceuticals
IT and Informatics Weekly New Product Roundup (weeks of Dec. 26 to Jan. 6)