Implementation of a parallel protein structure alignment service on cloud

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs

For biological applications, sequence alignment is an important strategy to analyze DNA and protein sequences. Multiple sequence alignment is an essential methodology to study biological data, such as homology modeling, phylogenetic reconstruction and etc. However, multiple sequence alignment is a NP-hard problem. In the past decades, progressive approach has been proposed to successfully align multiple sequences by adopting iterative pairwise alignments. Due to rapid growth of the next generation sequencing technologies, a large number of sequences can be produced in a short period of time. When the problem instance is large, progressive alignment will be time consuming. Parallel computing is a suitable solution for such applications, and GPU is one of the important architectures for contemporary parallel computing researches. Therefore, we proposed a GPU version of ClustalW v2.0.11, called CUDA ClustalW v1.0, in this work. From the experiment results, it can be seen that the CUDA ClustalW v1.0 can achieve more than 33× speedups for overall execution time by comparing to ClustalW v2.0.11.

Cloud computing for protein-ligand binding site comparison

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

Local alignment tool based on Hadoop framework and GPU architecture

With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single GPU. Therefore, we implement a distributed BLASTP by combining Hadoop and multi-GPUs. The experimental results present that the proposed method can improve the performance of BLASTP on single GPU, and also it can achieve high availability and fault tolerance.

Open reading frame phylogenetic analysis on the cloud

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.

Cloud computing-based TagSNP selection algorithm for human genome data

Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used.

Feature amplified voting algorithm for functional analysis of protein superfamily

BACKGROUND

Identifying the regions associated with protein function is a singularly important task in the post-genomic era. Biological studies often identify functional enzyme residues by amino acid sequences, particularly when related structural information is unavailable. In some cases of protein superfamilies, functional residues are difficult to detect by current alignment tools or evolutionary strategies when phylogenetic relationships do not parallel their protein functions. The solution proposed in this study is Feature Amplified Voting Algorithm with Three-profile alignment (FAVAT). The core concept of FAVAT is to reveal the desired features of a target enzyme or protein by voting on three different property groups aligned by three-profile alignment method. Functional residues of a target protein can then be retrieved by FAVAT analysis. In this study, the amidohydrolase superfamily was an interesting case for verifying the proposed approach because it contains divergent enzymes and proteins.

RESULTS

The FAVAT was used to identify critical residues of mammalian imidase, a member of the amidohydrolase superfamily. Members of this superfamily were first classified by their functional properties and sources of original organisms. After FAVAT analysis, candidate residues were identified and compared to a bacterial hydantoinase in which the crystal structure (1GKQ) has been fully elucidated. One modified lysine, three histidines and one aspartate were found to participate in the coordination of metal ions in the active site. The FAVAT analysis also redressed the misrecognition of metal coordinator Asp57 by the multiple sequence alignment (MSA) method. Several other amino acid residues known to be related to the function or structure of mammalian imidase were also identified.

CONCLUSIONS

The FAVAT is shown to predict functionally important amino acids in amidohydrolase superfamily. This strategy effectively identifies functionally important residues by analyzing the discrepancy between the sequence and functional properties of related proteins in a superfamily, and it should be applicable to other protein families.

GPU‐based parallel fuzzy c‐mean clustering model via genetic algorithm

Detection of white matter changes in brain tissue using magnetic resonance imaging has been an increasingly active and challenging research area in computational neuroscience. A genetic algorithm based on a fuzzy c‐mean clustering method (GAFCM) was applied to simulated images to separate foreground spot signal information from the background, and the results were compared. The strength of this algorithm was tested by evaluating the segmentation matching factor, coefficient of determination, concordance correlation, and gene expression values. The experimental results demonstrated that the segmentation ability of GAFCM was better than that of fuzzy c‐means and K‐means algorithms. However, GAFCM is computationally expensive. This study presents a new GPU‐based parallel GAFCM algorithm to improve the performance of GAFCM. The experimental results show that computational performance can be increased by a factor of approximately 20 over the CPU‐based GAFCM algorithm while maintaining the quality of the processed images. Thus, the proposed GPU‐based parallel GAFCM algorithm can achieve the same results and significantly decrease processing time. Copyright © 2015 John Wiley & Sons, Ltd.

Efficient bit‐parallel subcircuit extraction using CUDA

Wafer processing technology has been improving rapidly. Moore's law has been exceeded as the number of transistors in a dense integrated circuit, now increases threefold or more, approximately every year. The integrated circuit has gone from very large scale to giga large scale. The extraction of subcircuits has therefore become computation‐intensive. In this paper, we propose an efficient bit‐parallel subcircuit extraction algorithm using graphic processing units. We conducted experimental trials and demonstrated that the proposed algorithm can achieve high throughput, suggesting practical applications in the extraction of subcircuits. Copyright © 2015 John Wiley & Sons, Ltd.

The classification of stages of epiretinal membrane using convolutional neural network on optical coherence tomography image

BACKGROUND AND OBJECTIVE

The gold standard for diagnosing epiretinal membranes is to observe the surface of the internal limiting membrane on optical coherence tomography images. The stages of the epiretinal membrane are used to decide the condition of the health of the membrane. The stages are not detected because some of them are similar. To accurately classify the stages, a deep-learning technology can be used to improve the classification accuracy.

METHODS

A combinatorial fusion with multiple convolutional neural networks (CNN) algorithms are proposed to enhance the accuracy of a single image classification model. The proposed method was trained using a dataset of 1947 optical coherence tomography images diagnosed with the epiretinal membrane at the Taichung Veterans General Hospital in Taiwan. The images consisted of 4 stages; stages 1, 2, 3, and 4.

RESULTS

The overall accuracy of the classification was 84%. The combination of five and six CNN models achieves the highest testing accuracy (85%) among other combinations, respectively. Any combination with a different number of CNN models outperforms any single CNN algorithm working alone. Meanwhile, the accuracy of the proposed method is better than ophthalmologists with years of clinical experience.

CONCLUSIONS

We have developed an efficient epiretinal membrane classification method by using combinatorial fusion with CNN models on optical coherence tomography images. The proposed method can be used for screening purposes to facilitate ophthalmologists making the correct diagnoses in general medical practice.

Multiple genome sequences alignment algorithm based on coding regions

Multiple Sequence Alignment (MSA) is the computational biology tool for facilitating the study of DNA homology, phylogeny determinations and conserved motifs. Many MSA methods have been presented to align protein, DNA, and RNA sequences successfully but not for coding region sequences. Therefore, we propose a heuristic alignment method, CORAL-M, for multiple genome sequences, especially for coding regions. CORAL-M adopts a codon-based probabilistic filtration model and the local optimal alignment solution to align multiple genome sequences in linear time. The experimental results presents that CORAL-M can find more potential function sites than that of other commonly used tools by aligning Enterovirus strains.