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Comparison of genomes using high-performance parallel computing

N.F. Almeida, E.N. Caceres, C.E.R. Alves, S.W. Song
Proceedings. 15th Symposium on Computer Architecture and High Performance Computing  
In this paper we use high-performance parallel computing to compare the whole genomes of two organisms, namely Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris, each with more  ...  First we intend to exploit the high-performance power of a cluster of low-cost microcomputers, propose a parallel solution to this problem, and show its feasibility with implementation and performance  ...  The purpose of the paper is to show that with a high performance parallel approach, it is possible to explore new horizons and tread on new terrain, eventually paving the way for new discoveries.  ... 
doi:10.1109/cahpc.2003.1250332 dblp:conf/sbac-pad/AlmeidaACS03 fatcat:5yb5wfmjnjclveheapyhsmhyvy

Performance Study of a Whole Genome Comparison Tool on a Hyper-Threading Multiprocessor [chapter]

Juan del Cuvillo, Xinmin Tian, Guang R. Gao, Milind Girkar
2003 Lecture Notes in Computer Science  
This paper presents a performance evaluation of the whole genome comparison tool called ATGC -Another Tool for Genome Comparison, on a Hyper-Threading multiprocessor.  ...  We use our application to determine the system scalability for this particular type of sequence comparison algorithm and the improvement due to Hyper-Threading technology.  ...  This paper focuses on the parallel implementation and performance study of a whole genome comparison tool using OpenMP on the Intel architecture.  ... 
doi:10.1007/978-3-540-39707-6_40 fatcat:vewkmq323jgmlmjt4ha472xsra

Editorial: Special Section on High-Performance Computational Biology

S. Aluru, N.M. Amato, D.A. Bader
2006 IEEE Transactions on Parallel and Distributed Systems  
Such queries are used in applications such as multiple genome/proteome comparisons, and in finding genes in newly sequenced genomes.  ...  We broadly view high-performance computational biology as the development and application of high-performance computing techniques for extending the reach or scale of investigations in computational biology  ...  In "High-Performance Direct Pairwise Comparison of Large Genomic Sequences," Christopher Mueller, Mehmet Dalkilic, and Andrew Lumsdaine bring up many surprising issues that arise in developing a high-performance  ... 
doi:10.1109/tpds.2006.102 fatcat:y6lpybmg3fcclhrd2xoc73kfua

High-Performance Algorithm Engineering for Large-Scale Graph Problems and Computational Biology [chapter]

David A. Bader
2005 Lecture Notes in Computer Science  
Many large-scale optimization problems rely on graph theoretic solutions; yet high-performance computing has traditionally focused on regular applications with high degrees of locality.  ...  We describe our novel methodology for designing and implementing irregular parallel algorithms that attain significant performance on high-end computer systems.  ...  We achieved this speedup through a combination of parallelism and high-performance algorithm engineering.  ... 
doi:10.1007/11427186_3 fatcat:3bwy4zp3f5dgdonrjt2mi5opom

Parallelism-based approaches in computational biology: a view from diverse case studies

Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
2017 Cluster Computing  
This special issue brings together high-quality state-ofthe-art contributions about parallelism-based approaches in computational biology, from different points of view or perspectives, that is, from diverse  ...  Computational biology allows and encourages the application of many different parallelism-based approaches.  ...  Thus, much faster pairwise and multiple genome comparisons can be performed, what is really important with the ever-growing list of available genomes.  ... 
doi:10.1007/s10586-017-1037-7 fatcat:ptpiyxc6uzft3hzno7zyo5gtai

Parallel Processing for Scanning Genomic Data-Bases [chapter]

D. Lavenier, J.-L. Pacherie
1998 Advances in Parallel Computing  
Speeding up the scan can be managed using various strategies of parallelization. This paper presents two approaches carried on at irisa: systolic and distributed parallelization.  ...  The scan of a genomic data-base aims to detect similarities between dna or protein sequences. This is a time-consuming operation, especially when weak similarities are searched.  ...  This can be achieved by parallelizing the computation using two approaches: 1. computing the pairwise comparison task on a dedicated systolic array: in that case, the search algorithm is parallelized,  ... 
doi:10.1016/s0927-5452(98)80008-7 fatcat:2mlliwkacjarrebumbvfyeodyi

Parallel-META: efficient metagenomic data analysis based on high-performance computation

Xiaoquan Su, Jian Xu, Kang Ning
2012 BMC Systems Biology  
Most of the current metagenomic data analysis softwares were designed to be used on a single computer or single computer clusters, which could not match with the fast increasing number of large metagenomic  ...  Therefore, some deeper analysis of the metagenomic data, such as the comparison of different samples, would be feasible in the pipeline, and some of these functionalities have been included into the Parallel-META  ...  Acknowledgements We thank Huimin Li from USTC, Xingzhi Chang and YinheQiao of QIBEBT, CAS for their support in arrangement of computing facilities.  ... 
doi:10.1186/1752-0509-6-s1-s16 pmid:23046922 pmcid:PMC3403166 fatcat:tzqnv73xgvgfpbkldnhmhensay

Parallel Implementation of a Bioinformatics Pipeline for the Design of Pathogen Diagnostic Assays

Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski, Jaques Reifman
2009 2009 DoD High Performance Computing Modernization Program Users Group Conference  
Experimental validation of these probes with various Burkholderia genomes showed that nearly 80% of the designed fingerprints identify the intended targets. 2009 DoD High Performance Computing Modernization  ...  To design pathogen fingerprints, we developed TOFI (Tool for Oligonucleotide Fingerprint Identification), a high performance computing software pipeline that designs microarray probes for multiple related  ...  Acknowledgments This work was sponsored by the US Department of Defense High Performance Computing Modernization Program, under the High Performance Computing Software Applications Institutes initiative  ... 
doi:10.1109/hpcmp-ugc.2009.36 fatcat:zqu6osvgyjegpd72eyg4bnvzpu

High-Performance Direct Pairwise Comparison of Large Genomic Sequences

C. Mueller, M.M. Dalkilic, A. Lumsdaine
2006 IEEE Transactions on Parallel and Distributed Systems  
Many applications in Comparative Genomics lend themselves to implementations that take advantage of common high-performance features in modern microprocessors.  ...  This speedup introduces the opportunity of performing full pairwise comparisons on entire genomes on a much larger scale than previously possible.  ...  Acknowledgements Jeremiah Willcock, from the Open Systems Lab at Indiana University, helped prototype an early version of the algorithm and provided feedback during the development process.  ... 
doi:10.1109/tpds.2006.104 fatcat:4spnamo62rexnmtq5kqxrod33y

Fine-Grained Parallel Genomic Sequence Comparison [chapter]

Dominique Lavenier
2010 Parallel and Distributed Computing  
The performances of these parallel machines were impressive due to the high number of small processing units running in parallel.  ...  For genomic data mining applications which process billions of sequences, this approach cannot practically be used due to its very high computational complexity.  ...  Fine-Grained Parallel Genomic Sequence Comparison, Parallel and Distributed Computing, Alberto Ros (Ed.), ISBN: 978-953-307-057-5, InTech, Available from: http://www.intechopen.com/books/parallel-and-distributed-computing  ... 
doi:10.5772/9449 fatcat:ns22vyct3rdjre24cs33bjr7ue

RACER: Rapid and accurate correction of errors in reads

Lucian Ilie, Michael Molnar
2013 Computer applications in the biosciences : CABIOS  
To support our claims, we performed extensive comparison with the existing leading programs on a variety of real datasets. Availability: RACER is freely available for non-commercial use at  ...  Motivation: High-throughput next-generation sequencing technologies enable increasingly fast and affordable sequencing of genomes and transcriptomes, with a broad range of applications.  ...  ACKNOWLEDGEMENTS Performance evaluation has been performed using the facilities of the Shared Hierarchical Academic Research Computing Network (SHARCNET: www.sharcnet.ca) and Compute/Calcul Canada.  ... 
doi:10.1093/bioinformatics/btt407 pmid:23853064 fatcat:3cplmucqxbb27fsoglufxev7gu

Scalable and cost-effective NGS genotyping in the cloud

Yassine Souilmi, Alex K. Lancaster, Jae-Yoon Jung, Ettore Rizzo, Jared B. Hawkins, Ryan Powles, Saaïd Amzazi, Hassan Ghazal, Peter J. Tonellato, Dennis P. Wall
2015 BMC Medical Genomics  
COSMOS implements complex workflows making optimal use of high-performance compute clusters.  ...  While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care.  ...  Although this work was conducted on AWS, the COSMOS/GenomeKey runs equally well on traditional High-Performance Computing clusters.  ... 
doi:10.1186/s12920-015-0134-9 pmid:26470712 pmcid:PMC4608296 fatcat:7cum7elswnbgvigo2xqgp6nsjm

Parallel-META: A high-performance computational pipeline for metagenomic data analysis

Xiaoquan Su, Jian Xu, Kang Ning
2011 2011 IEEE International Conference on Systems Biology (ISB)  
Most of the current metagenomic data analysis softwares were designed to be used on a single computer, which could not match with the fast increasing number of large metagenomic projects' computational  ...  component of these genomes in the microbial community.  ...  ACKNOWLEDGMENTS We thank Huimin Li from USTC and Xingzhi Chang and Yinhe Qiao of QIBEBT, CAS for their support in arrangement of computing facilities.  ... 
doi:10.1109/isb.2011.6033151 fatcat:kzu4kbkrwvca7muxa6weivs5ae

The parallelism motifs of genomic data analysis

Katherine Yelick, Aydın Buluç, Muaaz Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven Hofmeyr, Oguz Selvitopi (+2 others)
2020 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.  ...  We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes.  ...  TABLE 1 1 A comparison of motifs for parallel computing, including our own set for genomic data analysis.  ... 
doi:10.1098/rsta.2019.0394 pmid:31955674 fatcat:kzujmq5u2refvhoovtb2ap5vha

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization

Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning, Zhang Zhang
2014 PLoS ONE  
Parallel-META 2.0 is an extended and improved version of Parallel-META 1.0, which enhances the taxonomical analysis using multiple databases, improves computation efficiency by optimized parallel computing  ...  Therefore, it could provide accurate taxonomical and functional analyses of the metagenomic samples in high-throughput manner and on large scale.  ...  Acknowledgments We thank NVIDIA for providing us with the high-performance computing hardware through QIBEBT-NVIDIA CUDA Research Center. Author Contributions  ... 
doi:10.1371/journal.pone.0089323 pmid:24595159 pmcid:PMC3940597 fatcat:7ghfuqll7rgm5ph7e5kxa7ayt4
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