Search results for "hmmer"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
162	John Paul Walters, Rohan Darole, Vipin Chaudhary	Improving MPI-HMMER's scalability with parallel I/O.	IPDPS	2009	DBLP DOI BibTeX RDF
112	Yanteng Sun, Peng Li 0031, Guochang Gu, Yuan Wen, Yuan Liu, Dong Liu	HMMer acceleration using systolic array based reconfigurable architecture.	FPGA	2009	DBLP DOI BibTeX RDF	reconfigurable., systolic array, acceleration, hmmer
104	Bhanu Rekapalli, Christian Halloy, Igor B. Zhulin	HSP-HMMER: a tool for protein domain identification on a large scale.	SAC	2009	DBLP DOI BibTeX RDF
104	Jizhu Lu, Michael Perrone, Kursad Albayraktaroglu, Manoj Franklin	HMMer-Cell: High Performance Protein Profile Searching on the Cell/B.E. Processor.	ISPASS	2008	DBLP DOI BibTeX RDF
92	John Paul Walters, Xiandong Meng, Vipin Chaudhary, Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt, Darran Nathan, Joseph I. Landman	MPI-HMMER-Boost: Distributed FPGA Acceleration.	J. VLSI Signal Process.	2007	DBLP DOI BibTeX RDF	FPGA, VLSI, MPI, database searching, profile hidden markov models, HMMER
85	Yanteng Sun, Peng Li, Guochang Gu, Yuan Wen, Yuan Liu, Dong Liu	Accelerating HMMer on FPGAs using systolic array based architecture.	IPDPS	2009	DBLP DOI BibTeX RDF
85	Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt	High Performance Database Searching with HMMer on FPGAs.	IPDPS	2007	DBLP DOI BibTeX RDF
85	John Paul Walters, Bashar Qudah, Vipin Chaudhary	Accelerating the HMMER Sequence Analysis Suite Using Conventional Processors.	AINA (1)	2006	DBLP DOI BibTeX RDF
84	Karl Jiang, Oystein Thorsen, Amanda E. Peters, Brian E. Smith, Carlos P. Sosa	An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System.	IEEE Trans. Parallel Distributed Syst.	2008	DBLP DOI BibTeX RDF	multiple master parallelization, genomic sequence-search, Hidden Markov models, bioinformatics, parallel implementation, massively parallel systems, HMMER
66	Joseph I. Landman, Joydeep Ray, John Paul Walters	Accelerating HMMer searches on Opteron processors with minimally invasive recoding.	AINA (2)	2006	DBLP DOI BibTeX RDF
58	Ben Wun, Jeremy Buhler, Patrick Crowley	Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor.	IEEE PACT	2005	DBLP DOI BibTeX RDF
46	John Paul Walters, Vidyananth Balu, Suryaprakash Kompalli, Vipin Chaudhary	Evaluating the use of GPUs in liver image segmentation and HMMER database searches.	IPDPS	2009	DBLP DOI BibTeX RDF
46	Avery Ching, Wu-chun Feng, Heshan Lin, Xiaosong Ma, Alok N. Choudhary	Exploring I/O Strategies for Parallel Sequence-Search Tools with S3aSim.	HPDC	2006	DBLP DOI BibTeX RDF	parallel HMMer tool, parallel I/O strategy, parallel sequence-search tool, S3aSim framework, computational biologist, sequence database segmentation, master-writing strategy, worker-writing strategy, mpiBLAST tool, pioBLAST tool, search algorithm, parallel file system
27	Martin Larralde, Georg Zeller	PyHMMER: a Python library binding to HMMER for efficient sequence analysis.	Bioinform.	2023	DBLP DOI BibTeX RDF
27	Simon C. Potter, Aurelien Luciani, Sean R. Eddy, Young Mi Park, Rodrigo Lopez, Robert D. Finn	HMMER web server: 2018 update.	Nucleic Acids Res.	2018	DBLP DOI BibTeX RDF
27	Hanyu Jiang, Narayan Ganesan	CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
27	Naeem Abbas, Steven Derrien, Sanjay V. Rajopadhye, Patrice Quinton, Alexandre Cornu, Dominique Lavenier	Combining execution pipelines to improve parallel implementation of HMMER on FPGA.	Microprocess. Microsystems	2015	DBLP DOI BibTeX RDF
27	Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy	HMMER web server: 2015 update.	Nucleic Acids Res.	2015	DBLP DOI BibTeX RDF
27	Hanyu Jiang, Narayan Ganesan	Fine-Grained Acceleration of HMMER 3.0 via Architecture-Aware Optimization on Massively Parallel Processors.	IPDPS Workshops	2015	DBLP DOI BibTeX RDF
27	Miguel Ferreira, Nuno Roma, Luís M. S. Russo	Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER.	BMC Bioinform.	2014	DBLP DOI BibTeX RDF
27	Samuel Ferraz, Nahri Moreano	Evaluating Optimization Strategies for HMMer Acceleration on GPU.	ICPADS	2013	DBLP DOI BibTeX RDF
27	Mohd Nazrin Md. Isa, Khaled Benkrid, Thomas Clayton	A novel efficient FPGA architecture for HMMER acceleration.	ReConFig	2012	DBLP DOI BibTeX RDF
27	Xiaoqiang Li, Wenting Han, Gu Liu, Hong An, Mu Xu, Wei Zhou, Qi Li 0034	A Speculative HMMER Search Implementation on GPU.	IPDPS Workshops	2012	DBLP DOI BibTeX RDF
27	Robert D. Finn, Jody Clements, Sean R. Eddy	HMMER web server: interactive sequence similarity searching.	Nucleic Acids Res.	2011	DBLP DOI BibTeX RDF
27	Sebastián Isaza, Ernst Houtgast, Georgi Gaydadjiev	HMMER Performance Model for Multicore Architectures.	DSD	2011	DBLP DOI BibTeX RDF
27	Saddam Quirem, Fahian Ahmed, Byeong Kil Lee	CUDA acceleration of P7Viterbi algorithm in HMMER 3.0.	IPCCC	2011	DBLP DOI BibTeX RDF
27	Toyokazu Takagi, Tsutomu Maruyama	Accelerating HMMER search using FPGA Grid.	PARCO	2011	DBLP DOI BibTeX RDF
27	Sebastián Isaza, Ernst Houtgast, Friman Sánchez, Alex Ramírez, Georgi Gaydadjiev	Scaling HMMER Performance on Multicore Architectures.	CISIS	2011	DBLP DOI BibTeX RDF
27	Enric Tejedor, Rosa M. Badia, Romina Royo, Josep Lluis Gelpí	Enabling HMMER for the Grid with COMP Superscalar.	ICCS	2010	DBLP DOI BibTeX RDF
27	Steven Derrien, Patrice Quinton	Hardware Acceleration of HMMER on FPGAs.	J. Signal Process. Syst.	2010	DBLP DOI BibTeX RDF
27	Juan Fernando Eusse Giraldo, Nahri Moreano, Ricardo Pezzuol Jacobi, Alba Cristina Magalhaes Alves de Melo	A HMMER hardware accelerator using divergences.	DATE	2010	DBLP DOI BibTeX RDF
27	Naeem Abbas, Steven Derrien, Sanjay V. Rajopadhye, Patrice Quinton	Accelerating HMMER on FPGA using parallel prefixes and reductions.	FPT	2010	DBLP DOI BibTeX RDF
27	Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer	Accelerating HMMER on GPUs by implementing hybrid data and task parallelism.	BCB	2010	DBLP DOI BibTeX RDF
27	Toyokazu Takagi, Tsutomu Maruyama	Accelerating HMMER search using FPGA.	FPL	2009	DBLP DOI BibTeX RDF
27	Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt	Integrating FPGA acceleration into HMMer.	Parallel Comput.	2008	DBLP DOI BibTeX RDF
27	John Paul Walters, Joseph I. Landman, Vipin Chaudhary	Optimized Cluster-Enabled HMMER Searches.	Grid Computing for Bioinformatics and Computational Biology	2007	DBLP DOI BibTeX RDF
27	Steven Derrien, Patrice Quinton	Parallelizing HMMER for Hardware Acceleration on FPGAs.	ASAP	2007	DBLP DOI BibTeX RDF
27	Markus Wistrand, Erik L. L. Sonnhammer	Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.	BMC Bioinform.	2005	DBLP DOI BibTeX RDF
27	Madelaine Marchin, Paul T. Kelly, Jianwen Fang	Tracker: continuous HMMER and BLAST searching.	Bioinform.	2005	DBLP DOI BibTeX RDF
27	Daniel Reiter Horn, Mike Houston, Pat Hanrahan	ClawHMMER: A Streaming HMMer-Search Implementation.	SC	2005	DBLP DOI BibTeX RDF	Bio Science, Brook, Programmable Graphics Hardware, GPU Computing, Stream Computing, Data Parallel Computing
27	Yasuyo Kofune, Takahiro Koita, Akira Fukuda	Performance Evaluation of MPI-HMMER on the OBIGrid.	PDPTA	2004	DBLP BibTeX RDF
27	Zemin Zhang, William I. Wood	A profile hidden Markov model for signal peptides generated by HMMER.	Bioinform.	2003	DBLP DOI BibTeX RDF
27	Luis Sánchez-Pulido, Yan P. Yuan, Miguel A. Andrade, Peer Bork	NAIL-Network Analysis Interface for Linking HMMER results.	Bioinform.	2000	DBLP DOI BibTeX RDF
27	Marcella A. McClure, Chris Smith, Pete Elton	Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation.	ISMB	1996	DBLP BibTeX RDF
27	Stuart King, Yanni Sun, James R. Cole, Sakti Pramanik	BLAST Tree: Fast Filtering for Genomic Sequence Classification.	BIBE	2010	DBLP DOI BibTeX RDF	component, Bioinformatics, Blast, Homology, Metagenomic, Trie, Hmmer
27	Rahul P. Maddimsetty, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Brandon Harris	Accelerator design for protein sequence HMM search.	ICS	2006	DBLP DOI BibTeX RDF	protein motif, hidden Markov model, HMMER
27	Mark McCallister, Michael Kutyna, Daniel B. Delgado	Implementing high-performance grid computing in student computer labs.	SIGUCCS	2004	DBLP DOI BibTeX RDF	cluster, parallel, grid, BLAST, computer lab, HMMER
19	Fabiana F. Araújo, Ângela M. A. Pinheiro, Kaio M. Farias, Bernadette Farias Lóscio, Diana M. Oliveira	FlagelLink: a decision support system for distributed flagellar data using data warehouse.	SAC	2008	DBLP DOI BibTeX RDF	flagellar ontology, data integration, bioinformatics, decision support system, data warehouse
19	Robert Henschel, Matthias S. Müller	I/O Induced Scalability Limits of Bioinformatics Applications.	BIBE	2007	DBLP DOI BibTeX RDF
19	Denise Fukumi Tsunoda, Heitor Silvério Lopes	Automatic motif discovery in an enzyme database using a genetic algorithm-based approach.	Soft Comput.	2006	DBLP DOI BibTeX RDF
19	Bouchra Bouqata, Christopher D. Carothers, Boleslaw K. Szymanski, Mohammed Javeed Zaki	VOGUE: A Novel Variable Order-Gap State Machine for Modeling Sequences.	PKDD	2006	DBLP DOI BibTeX RDF
19	Anton Bezuglov, Juan E. Vargas	Simulated Annealing Algorithm with Biased Neighborhood Distribution for Training Profile Models.	ISMIS	2006	DBLP DOI BibTeX RDF
19	Thomas Rattei, Mathias C. Walter, Roland Arnold, David P. Anderson, Hans-Werner Mewes	Using Public Resource Computing and Systematic Pre-calculation for Large Scale Sequence Analysis.	GCCB	2006	DBLP DOI BibTeX RDF	sequence similarity, protein homology, public resource computing, grid computing, sequence analysis, protein domain
19	Vipin Sachdeva, Michael Kistler, Evan Speight	Poster reception - Pairwise alignments on the cell processor.	SC	2006	DBLP DOI BibTeX RDF
19	Yan Liu 0002, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan	Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition.	RECOMB	2005	DBLP DOI BibTeX RDF
19	Fabiano Pazzini, Fernanda Oliveira, Jorge A. Guimarães, Hermes Luís Neubauer de Amorim	Prediction of Myotoxic and Neurotoxic Activities in Phospholipases A2 from Primary Sequence Analysis.	BSB	2005	DBLP DOI BibTeX RDF
19	Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, Hong-Qiang Wang, Xin Huang	A Novel Hybrid GA/SVM System for Protein Sequences Classification.	IDEAL	2004	DBLP DOI BibTeX RDF