The J Craig Venter Institute (JCVI) in Rockville, Massachusetts, has incorporated CLC Bio's accelerated versions of the algorithms Hmmpfam and Hmmsearch into its bioinformatics pipeline.
They will be used for functional annotation of proteins identified in metagenomics data.
The algorithms originate from Dr Sean Eddy's Hmmer package but their core parts have been accelerated by CLC Bio using single instruction, multiple data (SIMD) technology.
Dr Saul Kravitz, director of bioinformatics software at the JCVI, said: 'Given the ongoing acceleration in DNA sequencing capacity it is imperative for us to ensure that the bioinformatics pipelines we use to analyse sequencing data do not become bottlenecks to our researchers.
'The SIMD accelerated tools from CLC Bio have given us an increase in analysis capacity that we could easily implement and take advantage of in our annotation pipeline without any further hardware investments.' CLC bio's command-line tool, CLC Bioinformatics Cell, uses SIMD technology to parallelise and thereby accelerate bioinformatics algorithms - such as Hmmpfam, Hmmsearch, ClustalW, and Smith-Waterman - on Intel and AMD computer processors.
