78,097 Hits in 5.6 sec

High-Performance Direct Pairwise Comparison of Large Genomic Sequences

C. Mueller, M.M. Dalkilic, A. Lumsdaine
2006 IEEE Transactions on Parallel and Distributed Systems  
This speedup introduces the opportunity of performing full pairwise comparisons on entire genomes on a much larger scale than previously possible.  ...  For large genomic comparisons, these new algorithms achieve speedups of up to 14.4x over the sequential version.  ...  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

High-Performance Direct Pairwise Comparison of Large Genomic Sequences

C. Mueller, M. Dalkilic, A. Lumsdaine
19th IEEE International Parallel and Distributed Processing Symposium  
This speedup introduces the opportunity of performing full pairwise comparisons on entire genomes on a much larger scale than previously possible.  ...  For large genomic comparisons, these new algorithms achieve speedups of up to 14.4x over the sequential version.  ...  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/ipdps.2005.246 dblp:conf/ipps/MuellerDL05 fatcat:rmpzi2sdjzb4phx6vlutwxzvmm

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Jonathan Göke, Marcel H. Schulz, Julia Lasserre, Martin Vingron
2012 Computer applications in the biosciences : CABIOS  
and classification of genome-wide datasets.  ...  Conclusion: N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts028 pmid:22247280 pmcid:PMC3289921 fatcat:cffozdykarclzkgjd4rjpl5t3y

Computational methods for alternative splicing prediction

P. Bonizzoni
2006 Briefings in Functional Genomics & Proteomics  
Here, we provide an overview of current methods for the computational prediction of alternative splicing based on the alignment of genome and transcript sequences.  ...  The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity.  ...  In particular, the analysis of gene structure and the characterization of splicing events have been accomplished by the design of tools to perform pairwise alignments of genomic and transcript sequences  ... 
doi:10.1093/bfgp/ell011 pmid:16769678 fatcat:agpf2erqgbfnpmzfftlvs4svim

An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges

P. Chain
2003 Briefings in Bioinformatics  
A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application.  ...  Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.  ...  This work was performed under the auspices of the US Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.  ... 
doi:10.1093/bib/4.2.105 pmid:12846393 fatcat:3p5ybliqe5earn3hz4bmatuljy

Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations

Michael D. Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin
2017 Molecular Ecology  
The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes.  ...  We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains.  ...  Acknowledgements We offer our sincerest thanks to Eric Durand, Fernando Racimo, Rebekah Rogers, Melinda Yang, Amy Ko, and other members of the Center for Theoretical Evolutionary Genomics for their useful  ... 
doi:10.1111/mec.14188 pmid:28543951 fatcat:k7oe52jfvrabtbcrjko24kkm5a

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

Brejnev Muhizi Muhire, Arvind Varsani, Darren Patrick Martin, Jens H. Kuhn
2014 PLoS ONE  
during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences.  ...  The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome  ...  Acknowledgments The authors would like to thank the University of Cape Town's ICTS High Performance Computing team (, for providing access to its computer cluster.  ... 
doi:10.1371/journal.pone.0108277 pmid:25259891 pmcid:PMC4178126 fatcat:fusvot7ah5dklj2qaxoznvf7ka

A universal genomic coordinate translator for comparative genomics

Neda Zamani, Görel Sundström, Jennifer RS Meadows, Marc P Höppner, Jacques Dainat, Henrik Lantz, Brian J Haas, Manfred G Grabherr
2014 BMC Bioinformatics  
Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses.  ...  Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences.  ...  We thank Kerstin Lindblad-Toh, Leif Andersson, Jochen Wolf, and their respective groups for being early adopters of the Kraken technology.  ... 
doi:10.1186/1471-2105-15-227 pmid:24976580 pmcid:PMC4086997 fatcat:op7tpxouargghmwp3wndnnivia

A high-throughput pipeline for the design of real-time PCR signatures

Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski, Jaques Reifman
2010 BMC Bioinformatics  
Results: We present the Tool for PCR Signature Identification (TOPSI), a high-performance computing pipeline for the design of PCR-based pathogen diagnostic assays.  ...  TOPSI successfully designed PCR signatures common to 18 Staphylococcus aureus genomes in less than 14 hours using 98 cores on a high-performance computing system.  ...  DoD High Performance Computing Modernization Program, under the High Performance Computing Software Appli-cations Institutes Initiative. We thank Mr.  ... 
doi:10.1186/1471-2105-11-340 pmid:20573238 pmcid:PMC2905370 fatcat:uyp7nb2dbzdwbbbx76s25uskry

Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals [article]

Jeremiah J Faith, Alice Chen Liaw, Varun Aggarwala, Nadeem O Kaakoush, Thomas Borody, Hazel Mitchell, Michael A Kamm, Sudarshan Paramsothy, Evan S Snitkin, Ilaria Mogno
2020 bioRxiv   pre-print
Here we analyzed >1000 sequenced bacterial strains from the fecal microbiota of 47 individuals from two countries and combined them with >150,000 bacterial genomes from NCBI to quantify the strain population  ...  size of different bacterial species, as well as the frequency of finding the same strain colonized in unrelated individuals who had no opportunities for direct microbial strain transmission.  ...  Performing these 118 analyses with the other popular pairwise genome comparison method of Average Nucleotide 119 Identity (ANI) 5 yields similar results.  ... 
doi:10.1101/2020.10.17.343640 fatcat:ezkirsigmrd5bccnd6xb25m36q

Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons

I. Dubchak
2000 Genome Research  
Department of Energy contract DE-AC376SF00098 and NIH GM-5748202 (K.A.F.) The publication costs of this article were defrayed in part by payment of page charges.  ...  ACKNOWLEDGMENTS We thank Keith Lewis, Willow Dean, and Cathy Blankespoor for DNA sequencing and Nila Patil for valuable remarks on the manuscript.  ...  This is an important finding as it suggests that a large fraction of the high percent identity noncoding elements identified through H/M DNA comparison studies are conserved because of functional constraints  ... 
doi:10.1101/gr.142200 pmid:10984448 pmcid:PMC310906 fatcat:nis6yef5vvcb3g2bpvkoy5ltui

Breaking the computational barriers of pairwise genome comparison

Oscar Torreno, Oswaldo Trelles
2015 BMC Bioinformatics  
Conclusions: We have addressed the problem of pairwise and all-versus-all comparison of large sequences in general, greatly increasing the limits on input data size.  ...  Results: We have developed C libraries for pairwise sequence comparison within diverse architectures, ranging from commodity systems to high performance and cloud computing environments.  ...  In this document we report on GECKO (GEnome Comparison with K-mers Out-of-core), a modular application designed to identify collections of HSPs by pairwise genome comparison procedures, that can then be  ... 
doi:10.1186/s12859-015-0679-9 pmid:26260162 pmcid:PMC4531504 fatcat:wsg6hnleubcyjmulc7jomtgy2e

PanGraph: scalable bacterial pan-genome graph construction [article]

Nicholas Noll, Marco Molari, Richard Neher
2022 bioRxiv   pre-print
With the wide-spread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically.  ...  Reference genomes contain a fraction of the microbial pangenome, the set of genes observed within all isolates of a given species, and are thus blind to both the dynamics of the accessory genome, as well  ...  This study was funded by the University of Basel and the NSF.  ... 
doi:10.1101/2022.02.24.481757 fatcat:jubzs7h4qjelvh6h4qdgu7aj2e

A case study in genome-level fragment assembly

T. Chen, S. S. Skiena
2000 Bioinformatics  
Motivation: We use the fact of two teams independently sequencing the one megabase genome of Borrelia burgdorferi as an opportunity to study the accuracy of genomelevel assembly.  ...  Results: We compare the results of three different assembly programs (PHRAP, TIGR Assembler, and STROLL) on the DNA fragments used in both the Brookhaven and TIGR sequencing projects.  ...  Acknowledgements We thank Bill Studier and the rest of the Brookhaven group for interesting discussions on primer walking and sequencing.  ... 
doi:10.1093/bioinformatics/16.6.494 pmid:10980146 fatcat:s2o4cx4s3vdyro7bzq65zpirca

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

Christopher A. Lavender, Robert J. Gorelick, Kevin M. Weeks, Claus O. Wilke
2015 PLoS Computational Biology  
Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities.  ...  Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures.  ...  Performed the experiments: CAL RJG. Analyzed the data: CAL RJG. Contributed reagents/materials/analysis tools: RJG. Wrote the paper: CAL KMW.  ... 
doi:10.1371/journal.pcbi.1004230 pmid:25992893 pmcid:PMC4439019 fatcat:36nv3zep3bfkvcocbtz6jzooay
« Previous Showing results 1 — 15 out of 78,097 results