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An Asynchronous Gals Interface With Applications, Jennifer A. Smith
An Asynchronous Gals Interface With Applications, Jennifer A. Smith
Electrical and Computer Engineering Faculty Publications and Presentations
A low-latency asynchronous interface for use in globally-asynchronous locally-synchronous (GALS) integrated circuits is presented. The interface is compact and does not alter the local clocks of the interfaced local clock domains in any way (unlike many existing GALS interfaces). Two applications of the interface to GALS systems are shown. The first is a single-chip shared-memory multiprocessor for generic supercomputing use. The second is an application-specific coprocessor for hardware acceleration of the Smith-Waterman algorithm. This is a bioinformatics algorithm used for sequence alignment (similarity searching) between DNA or amino acid (protein) sequences and sequence databases such as the recently completed human …
Protein Family Classification Using Structural And Sequence Information, Jennifer A. Smith
Protein Family Classification Using Structural And Sequence Information, Jennifer A. Smith
Electrical and Computer Engineering Faculty Publications and Presentations
Protein family classification usually relies on sequence information (as in the case of hidden Markov models and position-specific scoring matrices) or on structural information where some sort of average positional error between the atomic locations is used. The positional error method requires that the structure of all the proteins to be classified is known. Sequence methods have the advantage that a much larger number of proteins can be classified (since far more sequences are know than structures). However, sequence methods discard a large amount of useful information contained in the structures of the subset of proteins in the family for …