Tag: GPU

MUMmerGPU 2.0 – High-throughput sequence alignment using GPU

MUMmerGPU 2.0

:: DESCRIPTION

MUMmerGPU is an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies.

::DEVELOPER

Michael Schatz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • nVidia Card

:: DOWNLOAD

MUMmerGPU

:: MORE INFORMATION

MUMmerGPU is an open source project.

Citation:

Cole Trapnell and Michael C. Schatz
Optimizing data intensive GPGPU computations for DNA sequence alignment
Parallel Computing 2009 35(8-9)429-440

ADEPT v1.0 – Domain Independent Sequence Alignment strategy for GPU architectures

ADEPT v1.0

:: DESCRIPTION

ADEPT is a GPU accelerated sequence alignment library for short DNA reads and protein sequences.

::DEVELOPER

Muaaz Gul Awan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ADEPT

:: MORE INFORMATION

Citation

Awan MG, Deslippe J, Buluc A, Selvitopi O, Hofmeyr S, Oliker L, Yelick K.
ADEPT: a domain independent sequence alignment strategy for gpu architectures.
BMC Bioinformatics. 2020 Sep 15;21(1):406. doi: 10.1186/s12859-020-03720-1. PMID: 32933482; PMCID: PMC7493400.

OSPREY 3.2.289 / gOSPREY – Computational Structure-based Protein Design / for GPU

OSPREY 3.2.289 / gOSPREY

:: DESCRIPTION

OSPREY (Open Source Protein REdesign for You)is a suite of programs for computational structure-based protein design.OSPREY is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.). OSPREY can also be used for predicting small-molecule inhibitors. With certain limitations, the current version of OSPREY can also model protein-protein and protein-peptide interactions.

gOSPREY is the abbreviation for Open Source Protein REdesign for You on a GPU. It enables the user to utilize a GPU to accelerate the procedure of protein design in a massive parallel fashion.

::DEVELOPER

Donald Lab at Duke University , Machine Learning and Computational Biology Group at Tsinghua University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

OSPREY , gOSPREY

:: MORE INFORMATION

Citation

An efficient parallel algorithm for accelerating computational protein design.
Zhou Y, Xu W, Donald BR, Zeng J.
Bioinformatics. 2014 Jun 15;30(12):i255-i263. doi: 10.1093/bioinformatics/btu264.

Frey KM, Georgiev I, Donald BR, Anderson AC.
Predicting resistance mutations using protein design algorithms.
Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13707-12. Epub 2010 Jul 19. PMID: 20643959

G-BLASTN 1.1 – GPU-accelerated Nucleotide Alignment tool

G-BLASTN 1.1

:: DESCRIPTION

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

::DEVELOPER

Xiaowen Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 G-BLASTN

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1384-91. doi: 10.1093/bioinformatics/btu047. Epub 2014 Jan 24.
G-BLASTN: accelerating nucleotide alignment by graphics processors.
Zhao K1, Chu X.

GDASC – A GPU Parallel based Server for Detecting Batch Factors

GDASC

:: DESCRIPTION

GDASC is a GPU-parallel based server used for identifying batches and classifying samples into different batches in a high dimensional gene expression dataset.

::DEVELOPER

ZHANG LAB @ NKU

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang X, Yi H, Wang J, Liu Z, Yin Y, Zhang H.
GDASC: a GPU parallel-based web server for detecting hidden batch factors.
Bioinformatics. 2020 Aug 15;36(14):4211-4213. doi: 10.1093/bioinformatics/btaa427. PMID: 32386292.

MaxSSmap v1 – GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence

MaxSSmap v1

:: DESCRIPTION

MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxSSmap

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.
MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.
Turki T1, Roshan U.

Chi8 v1 – GPU program for Detecting Significant Interacting SNPs with the Chi-square 8-df test

Chi8 v1

:: DESCRIPTION

Chi8 is a program that calculates the chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit.
Usman Roshan

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Chi8

:: MORE INFORMATION

Citation

Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
Al-Jouie A, Esfandiari M, Ramakrishnan S, Roshan U.
BMC Res Notes. 2015 Sep 14;8:436. doi: 10.1186/s13104-015-1392-5.

GeauxDock v2 – GPU Accelerated Molecular Docking

GeauxDock v2

:: DESCRIPTION

GeauxDock is an ultra-fast automated docking program, designed to predict how small ligands bind to pharmacologically relevant macromolecules. GeauxDock employs a novel hybrid force field and a Monte Carlo protocol for the efficient sampling of conformational space.

::DEVELOPER

The LONI Institute

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GeauxDock

:: MORE INFORMATION

Citation

GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field.
Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M.
J Comput Chem. 2015 Oct 15;36(27):2013-26. doi: 10.1002/jcc.24031. d

GPU-BLAST 1.1 – Sequence Alignment with GPUs

GPU-BLAST 1.1

:: DESCRIPTION

GPU-BLAST is an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.

::DEVELOPER

Sahinidis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++
  • CUDA

:: DOWNLOAD

GPU-BLAST

:: MORE INFORMATION

Citation

Panagiotis D. Vouzis and Nikolaos V. Sahinidis,
“GPU-BLAST: using graphics processors to accelerate protein sequence alignment,”
Bioinformatics, 2011 Vol. 27, no. 2, pages 182-188,

BALSA 2.0 – GPU Accelerated Integrated WGS and WES Secondary Analysis

BALSA 2.0

:: DESCRIPTION

BALSA is an integrated solution for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis.

::DEVELOPER

L3 Bioinformatics Limited

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GPU

:: DOWNLOAD

 BALSA

:: MORE INFORMATION

Citation

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.
Luo R, Wong YL, Law WC, Lee LK, Cheung J, Liu CM, Lam TW.
PeerJ. 2014 Jun 3;2:e421. doi: 10.7717/peerj.421.