A Scalable Coprocessor for Bioinformatic Sequence Alignments
نویسنده
چکیده
A hardware coprocessor for the rapid calculation of bioinformatic sequence alignments is presented. The coprocessor uses a globally-asynchronous locally-synchronous (GALS) design style which makes the coprocessor much easier to scale as CMOS feature sizes decrease. The coprocessor is intended to be implemented on a single integrated circuit along with a simple 32-bit RISC processor and memory system. The specific sequence alignment algorithm implemented is that of Smith and Waterman, but the general design strategy could be extended to other bioinformatic sequence alignment algorithms.
منابع مشابه
Bioinformatic Analysis of L-Asparaginase II from Citrobacter Freundii 1101, Erwinia Chrysanthemi DSM 4610, E. coli BL21 and Klebsiella Pneumoniae ATCC 10031
Backgroung and Aims: L-Asparaginase II is a cornerstone of treatment protocols for acute lymphoblastic leukemia. Only asparaginase II obtained from E. coli K12 and Erwinia chrysanthemi have been used in human as therapeutic drug. The therapeutic effects of asparaginase II from E. coli K12 and Erwinia chrysanthemi is accompanied by side effects. It is desirable to search for other asparaginase I...
متن کاملBioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database
BACKGROUND Hepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases. No publicly available, up-to-date, multiple sequence alignments, containing full-length and subgenomic fragments per genotype, are available. Such alignments are useful in many analysis applications, including data-mining and phylogenetic analyses. RESULTS By issuing a ...
متن کاملImproving Profile-Profile Alignments via Log Average Scoring
Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignmen...
متن کاملEvaluation of the anti-Salmonella Aptamer using Bioinformatic Tools and ELAA Method
Background: Identifying and measuring food pathogens and environmental samples require accurate and high-sensitivity and specific methods. In addition, Salmonella is a zoonotic bacteria that can directly cause human disease. The aim of this work is to develop anti-Salmonella aptamer using bioinformatic tools and enzyme-linked aptamer assay (ELAA) for assessment of affinity and identifying Salmo...
متن کاملDendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments
The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of in...
متن کامل