The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
In the last decades there is an exponential growth in the amount of genomic data that need to be analyzed. A very important problem in biology is the extraction of the biologically functional genomic DNA from the actual genome of the organisms. There have been proposed many computational biology algorithms that solve the gene finding problem which utilize various approaches; GlimmerHMM is considered...
Secondary structure prediction is a compute-intensive task that is used in many bioinformatics applications. In this paper we have selected two of the most well-known secondary structure prediction algorithms, the Predator and the Zuker algorithm, and we present two FPGA-based systems that implement them. Also, this paper presents different schemes of data reuse and data organization of structure...
The Sudoku simulated annealing solver -SSAS is a probabilistic Sudoku solver. The general design is capable of solving a Sudoku board of order up to fifteen (15 ?? 15 ?? 15 ?? 15). It has been designed and fully implemented on a Xilinx Virtex II Pro - based Digilent XUP board. The solver has a serial-port interface to download problems and upload results to a personal computer, according to the specifications...
An important biology problem is the decoding of the DNA and the extraction of useful genetic information. There are many bioinformatics algorithms that try to solve the gene finding problem and one of the most efficient is the Glimmer algorithm. In this paper, we present a hardware architecture that implements the Glimmer algorithm. The architecture was developed specifically for the capabilities...
As FPGA devices become larger, more coarse-grain modules coupled with large scale reconfigurable fabric become available, thus enabling new classes of applications to run efficiently, as compared to a general-purpose computer. This paper presents an architecture that benefits from the large number of DSP modules in Xilinx technology to implement massive floating point arithmetic. Our architecture...
Driven by novel biological wet lab techniques such as pyrosequencing there has been an unprecedented molecular data explosion. The growth of biological sequence data has significantly out-paced Moore's law. This development also poses new computational and architectural challenges for the field of phylogenetic inference, i.e., the reconstruction of evolutionary histories (trees) for a set of organisms...
BLAST is a very popular computational biology algorithm. Since it is computationally expensive it is a natural target for acceleration research, and many reconfigurable architectures have been proposed offering significant improvements. In this paper we approach the same problem with a different approach: we propose a BLAST algorithm preprocessor that efficiently identifies the portions of the database...
The Use of DNA micro-arrays helps scientist detecting several types of cancer at primitive stage. There is a great amount of data that have to be processed when using DNA micro-arrays by computational heavy algorithms. For these two reasons, the great scientific interest of the problem, and the heavy computational load of the algorithm, bioinformatics research community have proposed several approaches,...
DNA sequence comparison and database search have evolved in the last years as a field of strong competition between several reconfigurable hardware computing groups. In this paper we present a BLAST preprocessor that efficiently marks the parts of the database that may produce matches. Our prefiltering approach offers significant reduction in the size of the database that needs to be fully processed...
The most prevalent algorithm for DNA sequence matching is the BLAST algorithm. We have developed several FPGA-based architectures to speed up BLAST execution. In this work we present a new VLSI architecture as a followup to our reconfigurable logic-based architectures, and we compare the performance of several software and hardware implementations of BLAST.
In the course of rapid system prototyping of a large scale design and implementation of the BLAST algorithm for bioinformatics, we evaluated two different design methods. First, we used the "traditional" method of design with modeling in C and design and synthesis using VHDL. Second, we used the automated tools MATLAB/Simulink with two different design flows, i.e. the fully automated one...
The BLAST algorithm is the prevalent tool that is used by molecular biologists for DNA sequence matching and database search. In this work we demonstrate that with an appropriate reconfigurable architecture, BLAST performance can be improved with a single-chip solution 5 times over a specialized and optimized computer cluster, or 37 times over a single computer. These initial results account for I/O...
DNA sequence comparison is a computationally intensive problem, known widely since the competition for human DNA decryption. Database search for DNA sequence comparison is of great value to computational biologists. Several algorithms have been developed and implemented to solve this problem efficiently, but from a user base point of view the BLAST algorithm is the most widely used one. In this paper,...
A new, configurable architecture has been designed and built in order to serve as a platform for experimentation with active networks. This architecture, named PLATO, provides 4 physical bi-directional connections for ATM networks, large reconfigurable resources, 256 Mbytes SDRAM for buffer space, a PCI port, and auxiliary expansion ports. Several applications are presented for this platform, one...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.