A Fast Parallel K-Modes Algorithm for Clustering Nucleotide Sequences to Predict Translation Initiation Sites

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Guilherme Torres CastroHenrique Cota Freitas

Abstract

Predicting the location of the translation initiation sites (TIS) is an important problem of molecular biology. In this field, the computational cost for balancing non-TIS sequences is substantial and demands high-performance computing. In this article, we present an optimized version of the K-modes algorithm to cluster TIS sequences and a comparison with the standard K-means clustering. The adapted algorithm uses simple instructions and fewer computational resources to deliver a significant speedup without compromising the sequence clustering results. We also implemented two optimized parallel versions of the algorithm, one for graphics processing units (GPUs) and the other one for general-purpose multicore processors. In our experiments, the GPU K-modes's performance was up to 203 times faster than the respective sequential version for processing Arabidopsis thaliana sequence.

References

May 11, 1982·Nucleic Acids Research·G D StormoL M Gold
Jan 11, 2000·Nucleic Acids Research·K D Pruitt, D R Maglott
Apr 13, 2001·Bioinformatics·K Y YeungW L Ruzzo
Apr 13, 2001·Bioinformatics·B Dysvik, I Jonassen
Feb 16, 2002·Bioinformatics·Artemis G Hatzigeorgiou
Sep 24, 2008·Journal of Clinical Nursing·Namita SrivastavaUNKNOWN UK PICU Staffing Study
Apr 8, 2010·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Michael HäfnerAndreas Vécsei
Feb 26, 2013·BMC Bioinformatics·Michal Jamroz, Andrzej Kolinski
Jun 14, 2013·BMC Bioinformatics·Yongchu LiuHuaiqiu Zhu

❮ Previous
Next ❯

Software Mentioned

Open Multi -
Nvida
CUDA
GPU
Hadoop
Open Computing Language
CESUP
MPI
Nvidia
OpenMP

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.