Filters








242,375 Hits in 3.9 sec

Parallel sequence alignment in limited space

J A Grice, R Hughey, D Speck
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
This paper proposes several methods of computing sequence alignments with limited memory per processing element. The algorithms are also well-suited to serial implementation.  ...  Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated.  ...  The Kestrel project has been supported in part by funds granted by the Natural Sciences Division of the University of California, Santa Cruz.  ... 
pmid:7584431 fatcat:vv6yu3eh55fvzij6e2sg2sqxcq

Accelerated large-scale multiple sequence alignment

Scott Lloyd, Quinn O Snell
2011 BMC Bioinformatics  
Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications.  ...  Results: We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator.  ...  In Stage 3, traceback information from full pairwise alignment is required to align groups of sequences.  ... 
doi:10.1186/1471-2105-12-466 pmid:22151470 pmcid:PMC3310909 fatcat:7m6z7i2ozrfbne2gngau367vqu

An efficient solution for aligning huge DNA sequences

Ahmad M. Hosny, Howida A. Shedeed, Ashraf S. Hussein, Mohamed F. Tolba
2011 The 2011 International Conference on Computer Engineering & Systems  
Recently, many parallel solutions were proposed in order to accelerate the exact methods of aligning huge DNA sequences.  ...  The fundamental innovation in this work is developing efficient, linear space complexity, parallel solution to achieve the optimum alignment with relatively good performance.  ...  These limitations make GPUs impractical to be used in case of large scale sequences alignment.  ... 
doi:10.1109/icces.2011.6141059 fatcat:2esc64abqrhuzcneodwrpje2xa

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space [article]

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J Wheelan, Steven Salzberg, Alex Szalay
2014 bioRxiv   pre-print
Motivation: In computing pairwise alignments of biological sequences, software implementations employ a variety of heuristics that decrease the computational effort involved in computing potential alignments  ...  Results: We implemented a read aligner called A21 that exploits GPU-based parallel sort and reduction techniques to restrict the number of locations where potential alignments may be found.  ...  ACKNOWLEDGEMENTS We are grateful to David Luebke and Cliff Wooley of NVidia Corporation for their help in understanding some of the nuances of NVidia GPU hardware.  ... 
doi:10.1101/007641 fatcat:7oxca2pcmffn7jy7b4woqhraiq

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay
2015 PeerJ  
When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected  ...  Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.808 pmid:25780763 pmcid:PMC4358639 fatcat:jxjlbuw6drahvgvsuuxueopfcm

Parallel biological sequence comparison using prefix computations

Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra
2003 Journal of Parallel and Distributed Computing  
We present practical parallel algorithms using prefix computations for various problems that arise in pairwise comparison of biological sequences.  ...  The best known sequential algorithms solve these problems in Omn time and Om + n space, where m and n are the lengths of the two sequences.  ...  Acknowledgements The authors gratefully acknowledge valuable suggestions from the anonymous referees, and in particular, for pointing out an erroneous algorithm in an earlier draft of this paper.  ... 
doi:10.1016/s0743-7315(03)00010-8 fatcat:zgj5k2eiifahroeczu6oh6ek3y

Reduced space sequence alignment

J.Alicia Grice, Richard Hughey, Don Speck
1997 Bioinformatics  
It can be readily solved in O(n 2 ) time and 0{n 2 ) space on a serial machine, or in O(n) time with O(n) space per O(n) processing elements on a parallel machine.  ...  Results: This paper presents a family of methods for computing sequence alignments with reduced memory that are well suited to serial or parallel implementation.  ...  Alicia Grice was supported in part by a Patricia Roberts Harris Fellowship. This work was supported in part by National Science Foundation grants MIP-9423985, BIR-9408579 and CD A-9115268.  ... 
doi:10.1093/bioinformatics/13.1.45 fatcat:enwqdqip4najdn7wvsv3vff4n4

Sequence Alignment with Traceback on Reconfigurable Hardware

Scott Lloyd, Quinn O. Snell
2008 2008 International Conference on Reconfigurable Computing and FPGAs  
A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations.  ...  The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner.  ...  The global alignment algorithm presented in this paper overcomes the memory size and bandwidth limitations of FPGA accelerators and does not limit the sequence length by the number of PEs.  ... 
doi:10.1109/reconfig.2008.30 dblp:conf/reconfig/LloydS08 fatcat:2ns5ua54w5dxtcquhsxow427ya

Shared Memory and Hardware Utilizations for the Parallelization of Local Sequences Alignment using SW Algorithm: A Review

Manhal ElfadilEltayeeb, Muhammad S. Abd Latiff, Ismail Fuzi Isnin
2015 International Journal of Computer Applications  
It is becoming increasingly difficult to ignore the importance of aligning DNA and Protein sequences to infer properties of new sequences from well-known reference sequences established and sorted in genetics  ...  Many studies in recent years have focused on different implementations of Sequences Alignment Problems (SAP). However, researcher confused with the ambiguous classification of the SAP.  ...  However, the limitation of memory prohibitive in comparing long sequences, there is remains a need for powerful methods with large spaces.  ... 
doi:10.5120/20141-2257 fatcat:arg4ddbqsfbolbfdag6gwz75yy

Reconfigurable Architecture for Biological Sequence Comparison in Reduced Memory Space

Azzedine Boukerche, Jan M. Correa, Alba Cristina M. A. de Melo, Ricardo P. Jacobi, Adson F. Rocha
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
DNA sequence alignment is a very important problem in bioinformatics.  ...  The algorithm proposed by Smith-Waterman (SW) is an exact method that obtains optimal local alignments in quadratic space and time.  ...  On the other hand, the query sequence must be put in the systolic array that has limited space.  ... 
doi:10.1109/ipdps.2007.370438 dblp:conf/ipps/BoukercheCMJR07 fatcat:axbfi5v2kjeq7pf275kksm5jv4

Hardware Accelerated Sequence Alignment with Traceback

Scott Lloyd, Quinn O. Snell
2009 International Journal of Reconfigurable Computing  
A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations.  ...  The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner.  ...  The global alignment algorithm presented in this paper overcomes the memory size and bandwidth limitations of FPGA accelerators and does not limit the sequence length by the number of PEs.  ... 
doi:10.1155/2009/762362 fatcat:hupo7k65sbfafprfxil2e4bjum

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydin Buluc, Leonid Oliker, Katherine Yelick
2020 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS)  
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications.  ...  We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software.  ...  Instead of exploring the whole m × n space, the Xdrop algorithm searches only for alignments that results in a limited number of edits between the two sequences.  ... 
doi:10.1109/ipdps47924.2020.00055 dblp:conf/ipps/ZeniGEDSHBOY20 fatcat:u7epgingcvdlbahlgn6r7bmjly

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment [article]

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick
2020 arXiv   pre-print
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications.  ...  We also demonstrate a 2.3x LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software.  ...  Instead of exploring the whole m × n space, the Xdrop algorithm searches only for alignments that results in a limited number of edits between the two sequences.  ... 
arXiv:2002.05200v1 fatcat:tjjmevttabh47nk4wzej4zimhe

Supercomputing for the parallelization of whole genome analysis

M. J. Puckelwartz, L. L. Pesce, V. Nelakuditi, L. Dellefave-Castillo, J. R. Golbus, S. M. Day, T. P. Cappola, G. W. Dorn, I. T. Foster, E. M. McNally
2014 Bioinformatics  
Whole genome analysis requires the alignment and comparison of raw sequence data, and results in a computational bottleneck because of limited ability to analyze multiple genomes simultaneously.  ...  Motivation: The declining cost of generating DNA sequence is promoting an increase in whole genome sequencing, especially as applied to the human genome.  ...  INTRODUCTION With the advent of massively parallel DNA sequencing, the rate at which human genome variation can be determined is limited less by sequence generation but instead by the computational tools  ... 
doi:10.1093/bioinformatics/btu071 pmid:24526712 pmcid:PMC4029034 fatcat:zfbyftzrr5cjdnzqrtzxtprlti

SEAL: a divide-and-conquer approach for sequence alignment

Harini Kandadi, Ramazan Savas Aygün
2015 Network Modeling Analysis in Health Informatics and Bioinformatics  
Sequence similarity search and sequence alignment methods are fundamental steps in comparative genomics and have a wide spectrum of application in the field of medicine, agriculture and environment.  ...  Heuristic methods like BLAST run much faster but may not provide optimal alignments. In this paper, we introduce a novel sequence alignment algorithm, SEAL.  ...  ., 2011) method redesigns Needleman-Wunsch/Still-Waterman (NW/SW) algorithm that obtains optimal sequence alignment in quadratic time and space cost for parallelization to yield in O(m+n) complexity.  ... 
doi:10.1007/s13721-015-0096-z dblp:journals/netmahib/KandadiA15 fatcat:3eus3mov75gqdhrz6hqolpxsae
« Previous Showing results 1 — 15 out of 242,375 results