NONLINEAR FM INDEX APPLICATION FOR ALIGNMENT OF SHORT DNA SEQUENCES USING RE-PARAMETRIZATION OF ALGORITHMS

Fractals ◽  
2018 ◽  
Vol 26 (03) ◽  
pp. 1850023 ◽  
Author(s):  
D. PACHECO BAUTISTA ◽  
R. CARREÑO AGUILERA ◽  
E. CORTÉS PÉREZ ◽  
M. GONZÁLEZ PÉREZ ◽  
J. J. MEDEL ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Processing Speed ◽  
High Speed ◽  
Hardware Implementation ◽  
Massively Parallel Sequencing ◽  
Search Algorithm ◽  
Massively Parallel ◽  
Field Programmable ◽  
Very High ◽  
Computation Speed

An innovative reconfiguration application is proposed to re-calculate the parameters of the Ferragina and Manzini exact search algorithm (or FM indexes), using a modular and efficient hardware implementation to accelerate alignment programs of short DNA sequence reads. Although these programs use multi-core execution strategies or multiple computers, they have become slow considering the very high speed at which the new massively parallel sequencing machines produce the reads to be aligned. Consequently, a search for different ways to accelerate the alignment is crucial. The proposed design runs with software functions in a hybrid system, and has the ability to align millions of reads to reference as large as the human genome. Tests on the M505k325t card show that a single alignment core can accelerate the computation by a factor close to [Formula: see text] in relation to BWA. Due to the minor consumption of area and power, multiple alignment cores can fill the Field Programmable Gate Array (FPGA) by multiplying the computation speed. With a multiple-core implementation, the processing speed of the design outperforms applications that are accelerated by GPUs and competes with similar FPGA proposals whose cost is much higher.

scholarly journals SYNTHESIS AND FPGA–IMPLEMENTATION BASED NEURAL TECHNIQUE OF A NONLINEAR ADC MODEL

2014 ◽  
pp. 27-33
Author(s):  
Mounir Bouhedda ◽  
Mokhtar Attari
Keyword(s):  
Integrated Circuit ◽  
Field Programmable Gate Array ◽  
High Speed ◽  
Hardware Description Language ◽  
Description Language ◽  
Analog To Digital ◽  
Field Programmable ◽  
Hardware Description ◽  
Nonlinear Analog ◽  
Very High

The aim of this paper is to introduce a new architecture using Artificial Neural Networks (ANN) in designing a 6-bit nonlinear Analog to Digital Converter (ADC). A study was conducted to synthesise an optimal ANN in view to FPGA (Field Programmable Gate Array) implementation using Very High-speed Integrated Circuit Hardware Description Language (VHDL). Simulation and tests results are carried out to show the efficiency of the designed ANN.

A very-high-speed field-programmable gate array using metal-to-metal antifuse programmable elements

1992 ◽  
Vol 23 (7) ◽  
pp. 561-568 ◽  
Author(s):  
J. Birkner ◽  
A. Chan ◽  
H.T. Chua ◽  
A. Chao ◽  
K. Gordon ◽  
...  
Keyword(s):  
Field Programmable Gate Array ◽  
High Speed ◽  
Field Programmable ◽  
Gate Array ◽  
Very High

scholarly journals Cancer Genomics

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1162 ◽  
Author(s):  
Elaine Mardis
Keyword(s):  
Dna Sequences ◽  
Cancer Genomics ◽  
Massively Parallel Sequencing ◽  
Clinical Care ◽  
Clinical Applications ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Recent Developments ◽  
Knowledge Of Cancer ◽  
Human Genome Reference

Modern cancer genomics has emerged from the combination of the Human Genome Reference, massively parallel sequencing, and the comparison of tumor to normal DNA sequences, revealing novel insights into the cancer genome and its amazing diversity. Recent developments in applying our knowledge of cancer genomics have focused on the utility of these data for clinical applications. The emergent results of this translation into the clinical setting already are changing the clinical care and monitoring of cancer patients.

scholarly journals Optimization and Implementation of Synthetic Basis Feature Descriptor on FPGA

Electronics ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 391
Author(s):  
Dah-Jye Lee ◽  
Samuel G. Fuller ◽  
Alexander S. McCown
Keyword(s):  
High Speed ◽  
Feature Detection ◽  
Hardware Implementation ◽  
Feature Matching ◽  
Image Features ◽  
Image Feature ◽  
Superior Performance ◽  
Feature Descriptor ◽  
Binary Descriptors ◽  
Field Programmable

Feature detection, description, and matching are crucial steps for many computer vision algorithms. These steps rely on feature descriptors to match image features across sets of images. Previous work has shown that our SYnthetic BAsis (SYBA) feature descriptor can offer superior performance to other binary descriptors. This paper focused on various optimizations and hardware implementation of the newer and optimized version. The hardware implementation on a field-programmable gate array (FPGA) is a high-throughput low-latency solution which is critical for applications such as high-speed object detection and tracking, stereo vision, visual odometry, structure from motion, and optical flow. We compared our solution to other hardware designs of binary descriptors. We demonstrated that our implementation of SYBA as a feature descriptor in hardware offered superior image feature matching performance and used fewer resources than most binary feature descriptor implementations.

FPGA-Realization of Vector Control for PMSM Drives

2013 ◽  
Vol 311 ◽  
pp. 249-254
Author(s):  
Nguyen Vu Quynh ◽  
Ying Shieh Kung ◽  
Pham Van Dung ◽  
Kuan Yuen Liao ◽  
Sheng Wei Chen
Keyword(s):  
Vector Control ◽  
High Speed ◽  
Pulse Width Modulation ◽  
Control Method ◽  
Experimental System ◽  
Control Algorithms ◽  
Description Language ◽  
Field Programmable ◽  
Hardware Description ◽  
Very High

The design and implementation of a vector control for Permanent Magnetic Synchronous Motor (PMSM) based on Field Programmable Gate Array (FPGA) technology is presented in this paper. Firstly, a Space Vector Pulse Width Modulation (SVPWM) scheme, vector control method and PI controller are derived. Secondly, the Very-High-Speed IC Hardware Description Language (VHDL) is adopted to describe the behavior of the aforementioned control algorithms. Finally, an experimental system is setup to evaluate the effectiveness and correctness of the proposed vector controller for PMSM drives.

Hardware Implementation of AES Algorithm with Logic S-box

2017 ◽  
Vol 26 (09) ◽  
pp. 1750141 ◽  
Author(s):  
Soufiane Oukili ◽  
Seddik Bri
Keyword(s):  
Data Security ◽  
High Speed ◽  
Hardware Implementation ◽  
Network Applications ◽  
Aes Algorithm ◽  
Communication Techniques ◽  
High Speed Network ◽  
Cryptographic Algorithm ◽  
Hardware Implementations ◽  
Field Programmable

Cryptography has an important role in data security against known attacks and decreases or limits the risks of hacking information, especially with rapid growth in communication techniques. In the recent years, we have noticed an increasing requirement to implement cryptographic algorithms in fast rising high-speed network applications. In this paper, we present high throughput efficient hardware implementations of Advanced Encryption Standard (AES) cryptographic algorithm. We have adopted pipeline technique in order to increase the speed and the maximum operating frequency. Therefore, registers are inserted in optimal placements. Furthermore, we have proposed 5-stage pipeline S-box design using combinational logic to reach further speed. In addition, efficient key expansion architecture suitable for our proposed design is also presented. In order to secure the hardware implementation against side-channel attacks, masked S-box is introduced. The implementations had been successfully done by virtex-6 (xc6vlx240t) Field-Programmable Gate Array (FPGA) device using Xilinx ISE 14.7. Our proposed unmasked and masked architectures are very fast, they achieve a throughput of 93.73 Gbps and 58.57 Gbps, respectively. The obtained results are competitive in comparison with the implementations reported in the literature.

scholarly journals Support Vector Machine working on FPGA and the segmentation method of brain MR screening

2017 ◽  
Vol 4 (3) ◽  
pp. 120 ◽  
Author(s):  
Fatih Şişik ◽  
Eser Sert
Keyword(s):  
Integrated Circuit ◽  
Field Programmable Gate Array ◽  
High Speed ◽  
Hardware Description Language ◽  
Support Vector ◽  
Segmentation Method ◽  
Description Language ◽  
Field Programmable ◽  
Hardware Description ◽  
Very High

Alan Programlanabilir Kapı Dizileri (Field Programmable Gate Array-FPGA) programlanabilir sayısal bloklar ve bağlantılarını içeren cihazlar olup çok esnek ve hızlı çalışabilme özelliklerine sahiptir. Programlanabilen bu sayısal kapılar sayesinde karmaşık tasarımlar kolay bir şekilde geliştirilebilmektedir. FPGA’lar küçük boyutlarda olup bilgisayardan bağımsız mobil olarak ve bilgisayarlardan daha yüksek hızlarda çalışabilmektedirler. Veri madenciliğinin görevlerinden biri olan sınıflandırma probleminin çözümü için geliştirilmiş önemli makine öğrenimi algoritmalarından biri Destek Vektör Makineleri’ dir. Literatürde Destek Vektör Makineleri’ nin diğer birçok tekniğe göre daha başarılı sonuçlar verdiği kanıtlanmıştır. Tümör analizi, yüz tanıma, robotik göz oluşturma gibi konular, araştırmacıların görüntü işleme alanında yoğun olarak üzerinde çalıştıkları güncel, önemli ve zor problemlerden bazılarıdır. Bilgisayarda yapılan tümör analizinde, grafik ve resimlerin işlenmesinde yavaş işlem yapma ve aynı zamanda mobil olmama sorunlarından, FPGA donanımı ile görüntü işlemede bu sorunların üstesinden gelinmektedir. Bu çalışmada FPGA donanımında çalışan destek vektör makinası kullanılarak daha gerçekçi tümör analizi yapılarak tümörlü bölgelerin bulunması ve gerekli analiz sonuçlarının gösterilmesi amaçlanmaktadır. Böylece sağlık alanında da kullanılabilecek yararlı bir donanımın tasarımı gerçekleştirilecektir. Dolayısıyla gömülü sistemlerle anlatılan bu işlem süreçlerini gerçekleştiren çalışma sayısı çok az olduğundan çalışma özgün değer taşımaktadır. Buna ek olarak, FPGA’ ya özgü donanım tanımlama dillerinden biri olan Çok Yüksek Hızlı Tümleşik Devre Tanımlama Dili (Very High Speed Integrated Circuit  Hardware Description Language- VHDL) kullanılacaktır. Bölütleme sonucunun değerlendirilmesi için Uniformity Measure (UM) kullanılmıştır. UM değerlendirme sonucunun başarılı olduğu görülmüştür. Anahtar Kelimeler: Alan Programlanabilir Kapı Dizileri, FPGA, çok yüksek hızlı tümleşik devre tanımlama dili, vhdl, segmentasyon, destek vektör makinesi

scholarly journals FPGA Implementation of DTCWT and PCA Based Watermarking Technique

2018 ◽  
Vol 7 (2) ◽  
pp. 82
Author(s):  
M. S. Sudha ◽  
T. C. Thanuja
Keyword(s):  
Wavelet Transform ◽  
Field Programmable Gate Array ◽  
High Speed ◽  
Hardware Implementation ◽  
Image Watermarking ◽  
Software Implementation ◽  
Low Power Consumption ◽  
Complex Wavelet Transform ◽  
System Generator ◽  
Field Programmable

The hardware implementation of the image watermarking algorithm offers numerous distinct advantages over the software implementation in terms of low power consumption, less area usage and reliability. The advantages of Dual Tree Complex Wavelet Transform (DTCWT) and Principle Component Analysis (PCA) techniques are extracted to improve the robustness and perceptibility. The hardware watermarking solution is more economical, because adding the component only takes up a small dedicated area of silicon. The algorithm is developed and simulated using Matlab, Simulink and system generator. The implementation is carried out using Spartan 6 Diligent Atlys Field Programmable Gate array (FPGA). The architecture uses 256 slice registers, 257 slice Look Up Tables (LUT’s) and 47 I/O pins. It also meets the requirement of high speed architecture with a delay of 1.328ns and an operating frequency of 549.451MHz.

Ψηφιακή σχεδίαση και υλοποίηση κάρτας κρυπτογράφησης για μυστική επικοινωνία βασισμένη σε FPGA τεχνολογία

2009 ◽  
Author(s):  
Παναγιώτης Μαργαρώνης
Keyword(s):  
Integrated Circuits ◽  
High Speed ◽  
Linear Feedback ◽  
Description Language ◽  
Gate Arrays ◽  
Field Programmable ◽  
Programmable Gate Arrays ◽  
Hardware Description ◽  
Feedback Shift Register ◽  
Very High

Η παρούσα διατριβή παρουσιάζει τη διαδικασία σχεδίασης και υλοποίησης μιας ολοκληρωμένης και αυτόνομης κάρτας κρυπτογράφησης. Η συγκεκριμένη κάρτα έχει ονομαστεί LAM και εισάγει ένα ψηφιακό ολοκληρωμένο κύκλωμα το οποίο βασίζεται στο Peripheral Component Interconnection (PCI) δίαυλο. Η υλοποίηση της παραπάνω κάρτας κρυπτογράφησης σχεδιάστηκε με τη χρήση προγραμματιζόμενου ολοκληρωμένου κυκλώματος Field Programmable Gate Arrays (FPGA). Ο αντικειμενικός σκοπός της διατριβής είναι να προσφέρει σε βάθος γνώση αναφορικά με τη διαδικασία σχεδίασης και υλοποίησης ενός ψηφιακού κυκλώματος κρυπτογράφησης που βασίζεται στην τεχνολογία των ολοκληρωμένων προγραμματιζόμενων κυκλωμάτων FPGA με χρήση της γλώσσας περιγραφής υλικού Very High Speed Integrated Circuits Hardware Description Language (VHDL). Το συγκεκριμένο ψηφιακό κύκλωμα μπορεί να αξιοποιηθεί σαν κάρτα προσωπικού υπολογιστή. Η προαναφερόμενη κάρτα σχεδιάστηκε και υλοποιήθηκε σαν μια ολοκληρωμένη διαφανής συσκευή με δυνατότητα συμμετρικής κρυπτογράφησης/αποκρυπτογράφησης, ενσωματώνοντας ένα σύστημα δημιουργίας και διαχείρισης κλειδιών κρυπτογράφησης καθώς και συγχρονισμού με άλλες επικοινωνούντες συσκευές. Για την εκπόνηση της διατριβής πραγματοποιήθηκε μελέτη στα παρακάτω ερευνητικά πεδία. Στο πρώτο στάδιο μελετήθηκαν τα κυκλώματα FPGA, η γλώσσα περιγραφής υλικού VHDL, η κατανομή και ο χώρος σχεδίασης που περιλαμβάνει η υλοποίηση του κυκλώματος εσωτερικά στο Chip και τα εργαλεία υλοποίησης και ανάπτυξης. Στο δεύτερο στάδιο έγινε μελέτη των αρχών μετάδοσης δεδομένων μέσω του Internet, της κάρτας διασύνδεσης Ethernet και της επικοινωνίας πραγματικού χρόνου μέσω TCP/IP πρωτοκόλλου. Στο τρίτο στάδιο πραγματοποιήθηκε μελέτη στο μετασχηματισμό και μεταφορά κλειδιών από εξωτερική μνήμη στην εσωτερική μνήμη της κάρτας κρυπτογράφησης με τη βοήθεια Linear Feedback Shift Register (LFSR), στον προγραμματισμό LFSR και στην επιλογή κλειδιών (αδύναμα κλειδιά). Στο τέταρτο στάδιο μελετήθηκαν ερευνητικά θέματα που άπτονται της δημιουργίας και διαχείρισης κλειδιών συμμετρικής κρυπτογραφίας. Έπειτα έγινε μελέτη στη μετάδοση ψηφιακών δεδομένων μέσω πρωτοκόλλων DVB/DAB. Στη συνέχεια μελετήθηκε η εξουσιοδότηση χρήστη με Έξυπνες Κάρτες (Smart Cards) και το πρωτόκολλο ανάγνωσης των έξυπνων καρτών. Επιπλέον μελετήθηκαν η αρχιτεκτονική, οι αρχές επικοινωνίας του PCI διαύλου και ο χρονισμός του συστήματος, ενώ έγινε και ανάλυση των υπαρχόντων συμμετρικών αλγορίθμων κρυπτογράφησης που έχουν υλοποιηθεί σε επίπεδο υλικού. Ένα ακόμη πεδίο μελέτης υπήρξε ο συγχρονισμός των καρτών κρυπτογράφησης σε απομακρυσμένα συστήματα καθώς και η διάρκεια της ασφαλούς επικοινωνίας. Τέλος μελετήθηκαν οι βασικές αρχές για την προστασία από εξωτερικές παρεμβολές λόγω ηλεκτρομαγνητικής ακτινοβολίας καθώς και οι απαιτήσεις από εξωτερικά κυκλώματα για την ικανοποίηση των ηλεκτρικών απαιτήσεων της κάρτας.

A Very High Speed Field Programmable Gate Array-Based Sudoku Solver

2015 ◽  
Vol 21 (11) ◽  
pp. 3510-3514
Author(s):  
Nouar AlDahoul ◽  
Zaw Zaw Htike ◽  
Mouayad Zarzar
Keyword(s):  
Field Programmable Gate Array ◽  
High Speed ◽  
Field Programmable ◽  
Gate Array ◽  
Very High
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