9769309
Bioinformatic searches using a single-chip shared-memory multiprocessor
A single-chip shared-memory multiprocessor architecture is introduced which is particularly well suited to common bioinformatic computing tasks. The architecture uses asynchronous bus interfaces to create an integrated circuit design methodology allowing for scaling of the multiprocessor with very little design effort. A key aspect of this design methodology is that it is not necessary to expend significant design resources and chip area on the clock tree. An analysis of the Smith-Waterman alignment algorithm running on this architecture shows that the performance penalty due to increased bus latency compared to a fully synchronous architecture is negligible.
43472650
Covariance-Model-Based RNA Gene Finding: Using Dynamic Programming versus Evolutionary Computing
This chapter compares the traditional dynamic programming RNA gene finding methodolgy with an alternative evolutionary computation approach. Both methods take a set of estimated covariance model parameters for a non-coding RNA family as given. The difference lies in how the score of a database position with respect to the covariance model is computed. Dynamic programming returns an exact score at the cost of very large computational resource usage. Presently, databases are prefiltered using non-structural algorithms such as BLAST in order to make dynamic programming search feasible. The evolutionary computing approach allows for faster approximate search, but uses the RNA secondary structure information in the covariance model from the start.
23808436
Homology search with binary and trinary scoring matrices
Protein homology search can be accelerated with the use of bit-parallel algorithms in conjunction with constraints on the values contained in the scoring matrices. Trinary scoring matrices (containing only the values -1, 0, and 1) allow for significant acceleration without significant reduction in the receiver operating characteristic (ROC) score of a Smith-Waterman search. Binary scoring matrices (containing the values 0 and 1) result in some reduction in ROC score, but result in even more acceleration. Binary scoring matrices and five-bit saturating scores can be used for fast prefilters to the Smith-Waterman algorithm.
17217679
The Advanced Encryption Standard on an Asynchronous Shared-Memory Multiprocessor
The performance of a single-chip shared-memory multiprocessor system for encryption/decryption of large quantities of information is examined. The multiprocessor uses an asynchronous bus system to increase scalability and to reduce design effort. The target application is the Advanced Encryption Standard (AES) with 128 bit key. Chip area requirements and encryption/decryption throughput rates are examined.
12317353
Using Hydrophobicity Correlation Measures for Protein Family Classification
30143406
Performance of a GALS Single-Chip Multiprocessor
33128388
PULSAR: a personalized microcomputer-based system for keyword search and retrieval of literature information
(18) Kowalski, B. R.; Bender, C. F. “Pattern Recognition. 11. Linear and Nonlinear Methods for Displaying Chemical Data”. J. Am. Chem. Soc. (16) Everitt, B. S. “Unresolved Problems in Cluster Analysis”. Biometrics 1979. 35. 169-181. . . ., 1 (17) Williams, W. T.; Lance, G. N. “Hierarchical Classificatory Methods”. In “Statistical methods for Digital Computers”; Enslein, K., et al., Eids.; 1973, 95, 686-693. (19) Everitt, B. S.; “Graphical Techniques for Multivariate Data”; HeineWiley: New York, 1977; Va. 111. mann: 1978.