Biomatters Adds New Algorithms

April 10, 2011

By Bio-IT World Staff

April 11, 2011 | Biomatters' Geneious Server has added several new algorithms and improved capabilities to easily offload high-intensity processing to computer clusters straight from researchers’ desktops. Combined with the user-friendly Geneious Pro desktop software, researchers will have a wider choice of algorithms and direct access to the full power of their institution’s computing grid or cluster.

The popular LastZ, Glimmer, PAUP* and SOAP2 algorithms can now be launched from a desktop to run on Geneious Server or be scheduled to run on high-performance computing clusters. The addition of Load Sharing Facility (LSF) from Platform Computing, along with the existing Oracle’s SGE scheduling capabilities, means Geneious Server 1.1 now supports the two most popular computing cluster scheduling tools.

“If you want to run a large BLAST analysis from your laptop, now you can easily use Geneious Server as a staging device to schedule it to run on your own cluster.  Geneious Server puts both powerful hardware and powerful software tools into the hands of everyday researchers, who typically may only get occasional access” said Biomatters CEO Candace Kinser in a press release.

Geneious Sever 1.1 will support the powerful LastZ genome alignment and visualization tool, the widely-used phylogentics tool PAUP* and Glimmer for bacterial gene prediction, among others.

The DeCypher Acceleration module for Geneious Server will also let researchers offload large sequence comparison jobs such as BLAST, HMMer or Smith-Waterman to TimeLogic DeCypher cards for results in a fraction of the time compared to using conventional technologies.

Full genome assembly can be performed with data generated by Illumina, 454, SOLiD and Ion Torrent with support for Pacific Biosciences’ SMRT data under development.

“There is rarely one ‘magic-bullet’ algorithm in biological research, so we have given researchers a variety of ways to assemble their data rather than locking them in to a proprietary method that is not openly peer-reviewed,” said Kinser.