Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
TurboBLAST(r): A Parallel Implementation of BLAST Built on the TurboHub
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
BLAST++: a tool for BLASTing queries in batches
APBC '03 Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics 2003 - Volume 19
Real-Time Primer Design for DNA Chips
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Parallel genomic sequence-search on a massively parallel system
Proceedings of the 4th international conference on Computing frontiers
A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms
Journal of VLSI Signal Processing Systems
Mercury BLASTP: Accelerating Protein Sequence Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Hardware BLAST Algorithms with Multi-seeds Detection and Parallel Extension
ARC '08 Proceedings of the 4th international workshop on Reconfigurable Computing: Architectures, Tools and Applications
High speed biological sequence analysis with hiddenMarkov models on reconfigurable platforms
IEEE Transactions on Information Technology in Biomedicine - Special section on computational intelligence in medical systems
Design and implementation of a database filter for BLAST acceleration
Proceedings of the Conference on Design, Automation and Test in Europe
Some initial results on hardware BLAST acceleration with a reconfigurable architecture
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
FPGA based architecture for DNA sequence comparison and database search
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Biological sequence analysis with hidden markov models on an FPGA
ACSAC'05 Proceedings of the 10th Asia-Pacific conference on Advances in Computer Systems Architecture
Reconfigurable accelerator for the word-matching stage of BLASTN
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
| Hi-index | 0.01 |
Basic Local Alignment Search Tool (BLAST) is a standard computer application that molecular biologists use to search for sequence similarity in genomic databases. This report describes the implementation of an FPGAbased hardware implementation designed to accelerate the BLAST algorithm. FPGA-based custom computing machines, more widely known as Reconfigurable Computing, are supported by a number of vendors and the basic cost of FPGA hardware is dramatically decreasing. Hence, the main objective of this project is to explore the feasibility of using this new technology to realize a portable, Open Source FPGA-based accelerator for the BLAST Algorithm. The present design is targeted to an AceIIcard and the design is based on the latest version of BLAST available from NCBI. Since the entire application does not fit in hardware, a profile study was conducted that identifies the computationally intensive part of BLAST. An FPGA hardware component has been designed and implemented for this critical segment. The portability and cost-effectiveness of the design are discussed.