Name
Abstract | ||
|---|---|---|
This paper presents an in-depth look of how FPGA computing can offer substantial speedups in the execution of bioinformatics algorithms, with specific results achieved to date for a broad range of algorithms. Examples and case studies are presented for sequence comparison (BLAST, CAST), multiple sequence alignment (MAFFT, T-Coffee), RNA and protein secondary structure prediction (Zuker, Predator), gene prediction (Glimmer/GlimmerHMM) and phylogenetic tree computation (RAxML), running on mainstream FPGA technologies as well as high-end FPGA-based systems (Convey HC1, BeeCube). This work also presents technological and other obstacles that need to be overcome in order for FPGA computing to become a mainstream technology in Bioinformatics. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1109/BIBE.2012.6399733 | BIBE |
Keywords | Field | DocType |
multiple sequence alignment,bioinformatics algorithm,mainstream fpga technology,fpga computing,protein secondary structure prediction,broad range,mainstream technology,sequence comparison,convey hc1,gene prediction,genetics,proteins,field programmable gate arrays,bioinformatics,rna,computer architecture,prediction algorithms,algorithm design and analysis | Computer science,Prediction algorithms,Software,Artificial intelligence,Multiple sequence alignment,Computation,Protein secondary structure prediction,Algorithm design,Gene prediction,Field-programmable gate array,Algorithm,Bioinformatics,Machine learning | Conference |
Citations | PageRank | References |
0 | 0.34 | 0 |
Authors | ||
12 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Grigorios Chrysos | 1 | 38 | 9.88 |
| Theocharis Theocharides | 2 | 205 | 26.83 |
| Apostolos Dollas | 3 | 339 | 45.50 |
| Agathoklis Papadopoulos | 4 | 12 | 2.31 |
| Ioannis Kirmitzoglou | 5 | 5 | 1.17 |
| George Petihakis | 6 | 0 | 0.68 |
| Jacques Lagnel | 7 | 3 | 0.80 |
| Vasilis J. Promponas | 8 | 22 | 5.98 |
| George Kotoulas | 9 | 0 | 0.34 |
| Christos Rousopoulos | 10 | 0 | 0.34 |
| Panagiotis Vavylis | 11 | 0 | 0.34 |
| Euripides Sotiriades | 12 | 106 | 13.26 |