Inizio della pagina -
Logo DISCO
|
Visita la Versione ad elevata leggibilità
|
Vai al Contenuto della pagina
|
Vai alla Fine dei contenuti
|
Vai al Menu Principale
|
Vai alla Lista dei comandi
|
Vai al Menu inferiore
|
Logo Ateneo
   
Graphics Processing Units in Bioinformatics, Computational Biology and Systems Biology
This page contains a collection of GPU-powered software for Bioinformatics, Computational Biology and Systems Biology.
Researchers who developed a novel tool for GPUs in these disciplines, and wish it to be listed in this web page, are encouraged to contact us at the following address: daniela.besozzi@unimib.it.
Please cite this web page as:
Sequence alignment
Tool name Speed-up Parallel solution Reference
Sequence alignment based on Burrows-Wheeler Transform BarraCUDA - GPU Klus P. et al. 2012
Sequence alignment based on Burrows-Wheeler Transform CUSHAW - GPU Liu Y. et al. 2012
Sequence alignment based on Burrows-Wheeler Transform GPU-BWT - GPU Torres J. S. et al. 2012
Sequence alignment based on Burrows-Wheeler Transform SOAP3 - CPU-GPU Luo R. et al. 2013
Sequence alignment based on hash table SARUMAN - GPU Blom J. et al. 2011
Sequence alignment with gaps based on Burrows-Wheeler Transform SOAP3-dp - CPU-GPU Liu C. M. et al. 2012
Tool to map single nucleotide polymorphisms exploiting SOAP3-dp G-SNPM - CPU-GPU Manconi A. et al. 2014
Sequence alignment exploiting SOAP3-dp G-CNV 18✕ CPU-GPU Manconi A. et al. 2015
Alignment of gapped short reads with Bowtie2 algorithm nvBowtie 8✕ GPU Langmead B. et al. 2012
Alignment of gapped short reads with Bowtie2 algorithm MaxSSmap - GPU Turki T. et al. 2014
Reads assembly exploiting the Bruijn approach GPU-Euler 5✕ GPU Mahmood S. F. et al. 2011
Reads assembly exploiting the Bruijn approach MEGAHIT 2✕ GPU Li D. et al. 2015
Alignment of primary sequences with BLAST - 2✕ GPU Ling C. et al. 2010
Alignment of primary sequences with BLAST CUDA-BLASTP 6✕ GPU Liu W. et al. 2011
Alignment of primary sequences with BLAST G-BLASTN 14.8✕ GPU Zhao K. et al. 2014
Sequence alignment with Smith-Waterman method SW# - GPU Korpar M. et al. 2013
Sequence alignment with Smith-Waterman method PaSWAS - GPU Warris S. et al. 2015
Sequence alignment based on suffix tree MUMmerGPU 2.0 4✕ GPU Trapnell C. et al. 2009
Sequence similarity detection GPU_CAST 10✕ GPU Papadopoulos A. et al. 2013
Sequence similarity detection based on profiled Hidden Markov Models CUDAMPF 11-37✕ GPU Jiang H. et al. 2016
Multiple sequence alignment with Clustal CUDAClustal 2✕ GPU Pham H. P. et al. 2013
Multiple sequence alignment with Clustal GPU-REMuSiC - GPU Lin C. Y. et al. 2014
Molecular dynamics
Tool name Speed-up Parallel solution Reference
Non-bonded short-range interactions - 11✕ GPU Liu W. et al. 2008
Explicit solvent using the particle mesh Ewald scheme for the long-range electrostatic interactions - 2-5✕ GPU Salomon-Ferrer R. et al. 2013
Non-Ewald scheme for long-range electrostatic interactions - 100✕ multi-GPU Mashimo T. et al. 2013
Standard covalent and non-covalent interactions with implicit solvent OpenMM - GPU Eastman P. et al. 2012
Non-bonded and bonded interactions, charge equilibration procedure PuReMD 16✕ GPU Kylasa S. B. et al. 2014
Energy conservation for explicit solvent models MOIL-opt 10✕ CPU-GPU Ruymgaart A. P. et al. 2011
Electrostatics and generalized Born implicit solvent model LTMD 5.8✕ CPU-GPU Sweet J. C. et al. 2013
Molecular docking
Tool name Speed-up Parallel solution Reference
Hex spherical polar Fourier protein docking algorithm for rigid molecules - 45✕ CPU-GPU Ritchie D. W. et al. 2010
Conformation generation and scoring function for rigid and flexible molecules - 50✕ CPU-GPU Korb O. et al. 2011
High accuracy flexible molecular docking with differential evolution MolDock 27.4✕ GPU Simonsen M. et al. 2011
Large-scale protein structure alignment ppsAlign 39✕ CPU-GPU Pang B. et al. 2012
Protein-DNA docking with Monte Carlo simulation and simulated annealing - 28✕ GPU Wu J. et al. 2012
Katchalski-Katzir algorithm with traditional Fast Fourier transform rigid-docking scheme MEGADOCK - GPU Ohue M. et al. 2014
Docking approach using Ray Casting - 27✕ CPU-GPU Khar K. R. et al. 2013
Prediction and searching of molecular structures
Tool name Speed-up Parallel solution Reference
RNA secondary structure with dynamic programming - 17✕ GPU Rizk G. et al. 2009
RNA secondary structure with Zucker algorithm - 6.75 - 15.93✕ CPU-GPU Lei G. et al. 2012
Molecular distance geometry problem with a memetic algorithm MemHPG - CPU-GPU Nobile M. S. et al. 2014
Protein alignment GPU-CASSERT 180✕ GPU Mrozek D. et al. 2014
Protein alignment based on Simulated Annealing - - GPU Stivala A. D. et al. 2010
Simulation of the spatio-temporal dynamics and applications in Systems Biology
Tool name Speed-up Parallel solution Reference
Coarse-grain deterministic simulation with Euler method - 63✕ GPU Ackermann J. et al. 2009
Coarse-grain deterministic simulation with LSODA cupSODA 86✕ GPU Nobile M. S. et al. 2014
Coarse-grain deterministic and stochastic simulation with LSODA and SSA cuda-sim 47✕ GPU Zhou Y. et al. 2011
Coarse-grain stochastic simulation with SSA (with CUDA implementation of Mersenne-Twister RNG) - 50✕ GPU Li H. et al. 2010
Coarse- and fine-grain stochastic simulation with SSA - 130✕ GPU Sumiyoshi K. et al. 2015
Coarse-grain stochastic simulation with SSA - - GPU Klingbeil G. et al. 2012
Fine-grain stochastic simulation of large-scale models with SSA GPU-ODM - GPU Komarov I. et al. 2012
Fine-grain stochastic simulation with τ-leaping - 60✕ GPU Komarov I. et al. 2012
Coarse-grain stochastic simulation with τ-leaping cuTauLeaping 1,000✕ GPU Nobile M. S. et al. 2014
Reaction-diffusion simulation with SSA - - GPU Vigelius M. et al. 2011
Spatial τ-leaping simulation for crowded compartments STAUCC 24✕ GPU Pasquale G. et al. 2014
Particle-based methods for crowded compartments - 200✕ GPU Gladkov D. et al. 2011
Particle-based methods for crowded compartments - 135✕ GPU Dematté L. 2012
Agent-based model for cellular level dynamics FLAME - GPU Richmond P. et al. 2010
Agent-based model for cellular level dynamics - 100✕ GPU D'Souza R. M. et al. 2019
Parameter sweep analysis of blood coagulation cascade coagSODA 181✕ GPU Cazzaniga P. et al. 2014
Simulation of large-scale models with LSODA cupSODA*L - GPU Nobile M. S. et al. 2015
Parameter estimation with multi-swarm Particle Swarm Optimization - 24✕ GPU Nobile M. S. et al. 2012
Reverse engineering with Cartesian Genetic Programming cuRE - GPU Nobile M. S. et al. 2015
Parameter estimation and model selection with approximate Bayesian computation ABC-SysBio - GPU Liepe J. et al. 2010
Miscellaneous
Tool name Speed-up Parallel solution Reference
Identification of spectra in spectral analysis FastPaSS 8✕ GPU Baumgardner L. A. et al. 2011
Identification of spectra in spectral analysis Tempest 10✕ GPU Milloy J. A. et al. 2012
Identification of spectra in spectral analysis - 100✕ GPU Li Y. et al. 2012
Spectral analysis with wavelet transform - 200✕ GPU Hussong R. et al. 2009
Genome-wide interaction networks of co-expressed genes FastGCN 63✕ GPU Liang M. et al. 2014
Genome-wide gene-gene interaction analysis GBOOST 40✕ GPU Yung L. S. et al. 2011
Interacting SNP pairs detection PBOOST 60✕ GPU Yang G. et al. 2014
Haplotyping Mende-GPU - GPU Chen G. K. et al. 2012
Large-scale network robustness analysis PANET - GPU Trinh H. C. et al. 2014
Phylogenetic trees from DNA data MrBayes 63✕ (478✕*) GPU Bao J. et al. 2013
Phylogenetic Likelihood Library for DNA data PLL 2✕ GPU Izquierdo-Carrasco F. et al. 2013
Family-based sequencing data FamSeq 10✕ GPU Peng G. et al. 2014
Phylogenetic trees from DNA data oMC³ - CPU-GPU Chai J. et al. 2013
Heart wall tracking - - CPU-GPU Szafaryn L. G. et al. 2009
Quantum chemistry - 100✕ GPU Götz A. W. et al. 2010
Multi-objective optimization with Genetic Algorithm NSGA-II 10 ✕ - 130 ✕ GPU D'agostino et al. 2015
(C) Copyright 2016 - Dipartimento Informatica Sistemistica e Comunicazione - Viale Sarca, 336
20126 Milano - Edificio U14
redazioneweb@disco.unimib.it - ultimo aggiornamento di questa pagina 09/09/2016