High-throughput Protein Sequence Alignment on Multi-core Systems

Rapid evolution in sequencing technologies results in generating data on an enormous scale. A focal and main challenge in analyzing data at such a large scale is the alignment of the DNA/Protein sequences, whereby reads are compared to the reference sequences. To find similar sequences, alignment algorithms are used to align a query sequence with the database. Alignment algorithms can be utilized to classify the source of a sequence, to discover similarities among the organisms, or to deduce a progenitor connection. A wide range of algorithms for alignment has been developed in recent years.In this paper, an accurate method of accelerating such algorithms using GPUs has been investigated. A Swiss-Prot database has been processed using GPU implemented Smith-Waterman Sequence Alignment Algorithm. The first step in the process generates the alignment scores but not the actual alignment. Various available alignment tools like ssearch2 are then utilized to align the output file generated during the first step.The performance of GPU-accelerated implementation as compared to other techniques is then evaluated for performance /throughput improvement. Swiss-Prot database was aligned using various alignment tools. NVIDIA TESLA K40 GPU is being utilized for generating the results for this research. This implementation achieves the performance of 44.3 Giga cell updates per second (GCUPS), which is 22.9 times better than its implementation on GTX 275. Performance is improved as the workload of sequences of equal length is equally distributed among all the threads on Multiprocessors of GPU

Occurrence of RD149 and RD152 deletions in Mycobacterium tuberculosis strains from Pakistan

Introduction: Central Asian Strain 1 (CAS1) is the predominant Mycobacterium tuberculosis genotype in Pakistan. The occurrence of deletions in regions of differences (RDs) among CAS1 and other predominant genogroups in the country were investigated. Methodology: Using stratified random sampling, 235 M. tuberculosis (185 pulmonary, 50 extrapulmonary) strains were selected from 926 previously spoligotyped isolates, including 171 CAS strains (133 CAS1 (ST26), 38 CAS subfamily), 8 Beijing isolates, 47 isolates belonging to other previously defined ( Other ) clusters, and 9 previously undefined Unique isolates. Commonly reported RD deletions, RD1, RD750, RD207, RD149, RD152, RD105, RD150, RD142 and RD181, were investigated using a PCR - based method. Results: Deletions in RDs 750, 149 and 152 were identified among CAS strains, and in RDs 207, 149, 152, 105, 150, 142 and 181 in Beijing isolates. CAS1 strains showed more frequent RD149 deletions compared with CAS subfamily strains (p=0.036), and more frequent RD152 deletions compared with Other clusters (p=0.003). RD149 and RD152 deletions were more frequent in Beijing isolates compared with CAS1 strains (p \u3c 0.001). Concurrent RD149 and RD152 deletions were more frequent in CAS1 compared with Other clusters (p \u3c 0.001) and in Beijing strains compared with CAS1 (p \u3c 0.001). No significant difference was detected in RD deletion patterns between pulmonary and extra pulmonary isolates. Conclusion: Higher frequencies of RD149 and RD152 deletions and of concurrent RD149 and RD152 deletions were found in CAS1 and Beijing strains compared with CAS subfamilies, Other clusters and Unique strains. No association between these deletions and disease presentation, pulmonary or extrapulmonary tuberculosis, was observed

DOPA: GPU-based protein alignment using database and memory access optimizations

Background Smith-Waterman (S-W) algorithm is an optimal sequence alignment method for biological databases, but its computational complexity makes it too slow for practical purposes. Heuristics based approximate methods like FASTA and BLAST provide faster solutions but at the cost of reduced accuracy. Also, the expanding volume and varying lengths of sequences necessitate performance efficient restructuring of these databases. Thus to come up with an accurate and fast solution, it is highly desired to speed up the S-W algorithm. Findings This paper presents a high performance protein sequence alignment implementation for Graphics Processing Units (GPUs). The new implementation improves performance by optimizing the database organization and reducing the number of memory accesses to eliminate bandwidth bottlenecks. The implementation is called Database Optimized Protein Alignment (DOPA) and it achieves a performance of 21.4 Giga Cell Updates Per Second (GCUPS), which is 1.13 times better than the fastest GPU implementation to date. Conclusions In the new GPU-based implementation for protein sequence alignment (DOPA), the database is organized in equal length sequence sets. This equally distributes the workload among all the threads on the GPU's multiprocessors. The result is an improved performance which is better than the fastest available GPU implementation.MicroelectronicsElectrical Engineering, Mathematics and Computer Scienc

On the performance of video resolution, motion and dynamism in transmission using near-capacity transceiver for wireless communication

This article investigates the performance of various sophisticated channel coding and transmission schemes for achieving reliable transmission of a highly compressed video stream. Novel error protection schemes including Non-Convergent Coding (NCC) scheme, Non-Convergent Coding assisted with Differential Space Time Spreading (DSTS) and Sphere Packing (SP) modulation (NCDSTS-SP) scheme and Convergent Coding assisted with DSTS and SP modulation (CDSTS-SP) are analyzed using Bit Error Ratio (BER) and Peak Signal to Noise Ratio (PSNR) performance metrics. Furthermore, error reduction is achieved using sophisticated transceiver comprising SP modulation technique assisted by Differential Space Time Spreading. The performance of the iterative Soft Bit Source Decoding (SBSD) in combination with channel codes is analyzed using various error protection setups by allocating consistent overall bit-rate budget. Additionally, the iterative behavior of SBSD assisted RSC decoder is analyzed with the aid of Extrinsic Information Transfer (EXIT) Chart in order to analyze the achievable turbo cliff of the iterative decoding process. The subjective and objective video quality performance of the proposed error protection schemes is analyzed while employing H.264 advanced video coding and H.265 high efficient video coding standards, while utilizing diverse video sequences having different resolution, motion and dynamism. It was observed that in the presence of noisy channel the low resolution videos outperforms its high resolution counterparts. Furthermore, it was observed that the performance of video sequence with low motion contents and dynamism outperforms relative to video sequence with high motion contents and dynamism. More specifically, it is observed that while utilizing H.265 video coding standard, the Non-Convergent Coding assisted with DSTS and SP modulation scheme with enhanced transmission mechanism results in Eb/N0 gain of 20 dB with reference to the Non-Convergent Coding and transmission mechanism at the objective PSNR value of 42 dB. It is important to mention that both the schemes have employed identical code rate. Furthermore, the Convergent Coding assisted with DSTS and SP modulation mechanism achieved superior performance with reference to the equivalent rate Non-Convergent Coding assisted with DSTS and SP modulation counterpart mechanism, with a performance gain of 16 dB at the objective PSNR grade of 42 dB. Moreover, it is observed that the maximum achievable PSNR gain through H.265 video coding standard is 45 dB, with a PSNR gain of 3 dB with reference to the identical code rate H.264 coding scheme.Web of Science235art. no. 56

Extensively Drug-Resistant Tuberculosis, Pakistan

Frequency of extensively drug-resistant tuberculosis in Pakistan increased from 1.5% in 2006 to 4.5% in 2009 (p<0.01). To understand the epidemiology, we genotyped selected strains by using spoligotyping, mycobacterial interspersed repetitive units–variable number of tandem repeats, and IS6110 restriction fragment length polymorphism analysis

Production, optimization, and physicochemical characterization of biodiesel from seed oil of indigenously grown Jatropha curcas

With the growing demand for vegetable oils, alternative non-edible feedstocks like Jatropha curcas seed oil have gained interest for biodiesel production. The study aimed to comprehensively evaluate the physicochemical properties and biodiesel production potential of locally produced J. curcas seeds in Pakistan. Two different approaches were applied: a chemical synthesis approach involving acidic pretreatment and alkaline transesterification, and a biosynthetic approach using a lipase-producing strain of the Bacillus subtilis Q5 strain. The microbial biosynthesized biodiesel was further optimized using the Plackett–Burman design. The physicochemical properties of the J. curcas methyl esters were analyzed to assess their suitability as biodiesel fuel. Initially, the raw oil had a high free fatty acid content of 13.11%, which was significantly reduced to 1.2% using sulfuric acid pretreatment, keeping the oil to methanol molar ratio to be 1:12. Afterward, alkaline transesterification of purified acid-pretreated seed oil resulted in 96% biodiesel yield at an oil to methanol molar ratio of 1:6, agitation of 600 revolutions per minute (RPM), temperature 60°C, and time 2 h. Moreover, alkaline transesterification yielded ∼98% biodiesel at the following optimized conditions: oil to methanol molar ratio 1:6, KOH 1%, time 90 min, and temperature 60°C. Similarly, the Bacillus subtilis Q5 strain yielded ∼98% biodiesel at the following optimized conditions: oil: methanol ratio of 1:9, agitation 150 RPM, inoculum size 10%, temperature 37°C, and n-hexane 10%. The fuel properties of J. curcas seed biodiesel are closely related to standard values specified by the American Society for Testing and Materials (ASTM D6751–20a), indicating its potential as a viable biodiesel fuel source