Mitrion Applied
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With the advent of personal genomics, an individual’s hereditary material, or genome, can be interpreted to provide optimal choices for healthy living, as well as diagnosis, therapy and cure of diseases. All depends on revealing genome information by sequencing the 3.1 billion base pairs in human genome, and by interpreting its structure and function.
Personal genome sequences need to be analyzed by sophisticated computer algorithms run on computers that are faster than ever before, because of the exceptionally large amount of information generated by next generation sequencing systems.
Today, some genome computing tasks take days, weeks or even months. In the future, these task must be completed in seconds or minutes in order to be used in medical decisions.
Challenge
The challenge is to shorten genome computing processes by several orders of magnitude, while at the same time keeping system size and power consumption as low as possible.
Mitrion Solutions
Genome data is typically encoded using two bits per nucleotide base pair. The Mitrion Virtual Processor supports flexible data types that allow highly efficient processing of the nucleotide data. The Mitrion Platform is used to accelerate applications and algorithms such as:
NCBI BLAST-N - NCBI BLAST is the most used sequence alignment application available. Within the framework of the Mitrion-C Open Bio Project, Mitrionics has accelerated the BLAST-N nucleotide search algorithm to provide up to 60 times the performance of an unaccelerated solution. Click here for details on the Mitrion implementation of NCBI BLAST-N.
Tree of Life - Evolutionary history is a central problem in genomic research. With Mitrion, Markov Chain Monte Carlo Simulations for phylogenetic tree research have been accelerated by a factor of 15.
Other sequencing alignment codes being explored for MVP acceleration are:
Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.
SOAP is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology.
HMMer - Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
Smith-Waterman - is a well-known algorithm for performing local sequence alignment; that is, for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.
Personal genome sequences need to be analyzed by sophisticated computer algorithms run on computers that are faster than ever before, because of the exceptionally large amount of information generated by next generation sequencing systems.
Today, some genome computing tasks take days, weeks or even months. In the future, these task must be completed in seconds or minutes in order to be used in medical decisions.
Challenge
The challenge is to shorten genome computing processes by several orders of magnitude, while at the same time keeping system size and power consumption as low as possible.
Mitrion Solutions
Genome data is typically encoded using two bits per nucleotide base pair. The Mitrion Virtual Processor supports flexible data types that allow highly efficient processing of the nucleotide data. The Mitrion Platform is used to accelerate applications and algorithms such as:
NCBI BLAST-N - NCBI BLAST is the most used sequence alignment application available. Within the framework of the Mitrion-C Open Bio Project, Mitrionics has accelerated the BLAST-N nucleotide search algorithm to provide up to 60 times the performance of an unaccelerated solution. Click here for details on the Mitrion implementation of NCBI BLAST-N. Tree of Life - Evolutionary history is a central problem in genomic research. With Mitrion, Markov Chain Monte Carlo Simulations for phylogenetic tree research have been accelerated by a factor of 15.Other sequencing alignment codes being explored for MVP acceleration are:
Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. SOAP is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. HMMer - Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. Smith-Waterman - is a well-known algorithm for performing local sequence alignment; that is, for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.