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FCCM
2006
IEEE
137views VLSI» more  FCCM 2006»
15 years 4 months ago
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
Abstract: Approximate string matching is fundamental to bioinformatics, and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA imple...
Martin C. Herbordt, Josh Model, Yongfeng Gu, Bhara...
IPPS
2006
IEEE
15 years 4 months ago
Implementation of a programmable array processor architecture for approximate string matching algorithms on FPGAs
Approximate string matching problem is a common and often repeated task in information retrieval and bioinformatics. This paper proposes a generic design of a programmable array p...
Panagiotis D. Michailidis, Konstantinos G. Margari...
IPPS
2006
IEEE
15 years 4 months ago
MT-ClustalW: multithreading multiple sequence alignment
ClustalW is the most widely used tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three stages: pairwise alignment, guide tree generation ...
K. Chaichoompu, Surin Kittitornkun, Sissades Tongs...
IV
2006
IEEE
125views Visualization» more  IV 2006»
15 years 4 months ago
Visualization of Lattice-Based Protein Folding Simulations
Analysis of the spacial structure of proteins including folding processes is a challenge for modern bioinformatics. Due to limited experimental access to folding processes, comput...
Sebastian Potzsch, Gerik Scheuermann, Peter F. Sta...
INFOSCALE
2006
ACM
15 years 4 months ago
Scalable hardware accelerator for comparing DNA and protein sequences
Abstract— Comparing genetic sequences is a well-known problem in bioinformatics. Newly determined sequences are being compared to known sequences stored in databases in order to ...
Philippe Faes, Bram Minnaert, Mark Christiaens, Er...