IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Integrating GPU-accelerated sequence alignment and SNP detection for genome resequencing analysis
SSDBM'12 Proceedings of the 24th international conference on Scientific and Statistical Database Management
Kernel Weaver: Automatically Fusing Database Primitives for Efficient GPU Computation
MICRO-45 Proceedings of the 2012 45th Annual IEEE/ACM International Symposium on Microarchitecture
Methodological Review: 'Big data', Hadoop and cloud computing in genomics
Journal of Biomedical Informatics
FPGA-based hardware acceleration for local complexity analysis of massive genomic data
Integration, the VLSI Journal
Hi-index | 3.84 |
Motivation: The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53 000 citations that this software has received in the past two decades, and the use of the word ‘blast’ as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases. Results: Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST. The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4. Availability: The source code of GPU-BLAST is freely available at http://archimedes.cheme.cmu.edu/biosoftware.html. Contact: sahinidis@cmu.edu Supplementary information:Supplementary data are available at Bioinformatics online.