GHOSTM: a GPU-accelerated homology search tool for metagenomics.

PloS One
Shuji SuzukiYutaka Akiyama

Abstract

A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, faster search tools, such as BLAT, do not have sufficient search sensitivity for metagenomic analysis. Thus, a sensitive and efficient homology search tool is in high demand for this type of analysis. We developed a new, highly efficient homology search algorithm suitable for graphics processing unit (GPU) calculations that was implemented as a GPU system that we called GHOSTM. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 and 407 times faster than BLAST with 1 GPU and 4 GPUs, respectively. The system also showed higher search sensitivity and had a calculation speed that was 4...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 24, 1997·Science·R L TatusovD J Lipman
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Apr 5, 2002·Genome Research·W James Kent
Apr 15, 2003·Bioinformatics·Klaus Reichard, Michael Kaufmann
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Oct 13, 2005·The FEBS Journal·Stephen F AltschulYi-Kuo Yu
Dec 31, 2005·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Dec 22, 2006·Nature·Peter J TurnbaughJeffrey I Gordon
Oct 6, 2007·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Ken KurokawaMasahira Hattori
Mar 1, 2008·BMC Bioinformatics·Andrew D SmithMichael Q Zhang
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Nov 3, 2009·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Nov 19, 2009·Nucleic Acids Research·Robert D FinnAlex Bateman
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Mar 3, 2010·PLoS Computational Biology·John C WooleyIddo Friedberg
Nov 23, 2010·Bioinformatics·Panagiotis D Vouzis, Nikolaos V Sahinidis
Feb 23, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Weiguo LiuWolfgang Müller-Wittig

❮ Previous
Next ❯

Citations

Aug 31, 2014·Bioinformatics·Sergey L SheetlinJohn L Spouge
Dec 17, 2014·BMC Bioinformatics·Masahiro YanoKen Kurokawa

❮ Previous
Next ❯

Software Mentioned

HMMER
GPU
RMAP
BLASTP
GHOSTM CUDA
BLASTX
Bowtie
GHOSTM ( HOmology Search Tool for Metagenomics
CUDA
Solexa

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.