Parallel Smith-Waterman Algorithm for Gene Sequencing

Smith-Waterman Algorithm represents a highly robust and efficient parallel computing system development for biological gene sequence. The research work here gives a deep understanding and knowledge transfer about exiting approach for gene sequencing and alignment using Smith-waterman their strength and weaknesses. Smith-Waterman algorithm calculates the local alignment of two given sequences used to identify similar RNA, DNA and protein segments. To identify the enhanced local alignments of biological gene pairs Smith-Waterman algorithm uses dynamic programming approach. It is proficient in finding the optimal local alignment considering the given scoring system. DOI: 10.17762/ijritcc2321-8169.150515

Sensitive Long-Indel-Aware Alignment of Sequencing Reads

The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed genom-wide discovery of variations beyond single-nucleotide polymorphisms (SNPs), in particular of structural variations (SVs) like deletions, insertions, duplications, translocations, inversions, and even more complex rearrangements. Here, we design a read aligner with special emphasis on the following properties: (1) high sensitivity, i.e. find all (reasonable) alignments; (2) ability to find (long) indels; (3) statistically sound alignment scores; and (4) runtime fast enough to be applied to whole genome data. We compare performance to BWA, bowtie2, stampy and find that our methods is especially advantageous on reads containing larger indels

The Panchromatic Hubble Andromeda Treasury

The Panchromatic Hubble Andromeda Treasury (PHAT) is an on-going HST Multicycle Treasury program to image ~1/3 of M31's star forming disk in 6 filters, from the UV to the NIR. The full survey will resolve the galaxy into more than 100 million stars with projected radii from 0-20 kpc over a contiguous 0.5 square degree area in 828 orbits, producing imaging in the F275W and F336W filters with WFC3/UVIS, F475W and F814W with ACS/WFC, and F110W and F160W with WFC3/IR. The resulting wavelength coverage gives excellent constraints on stellar temperature, bolometric luminosity, and extinction for most spectral types. The photometry reaches SNR=4 at F275W=25.1, F336W=24.9, F475W=27.9, F814W=27.1, F110W=25.5, and F160W=24.6 for single pointings in the uncrowded outer disk; however, the optical and NIR data are crowding limited, and the deepest reliable magnitudes are up to 5 magnitudes brighter in the inner bulge. All pointings are dithered and produce Nyquist-sampled images in F475W, F814W, and F160W. We describe the observing strategy, photometry, astrometry, and data products, along with extensive tests of photometric stability, crowding errors, spatially-dependent photometric biases, and telescope pointing control. We report on initial fits to the structure of M31's disk, derived from the density of RGB stars, in a way that is independent of the assumed M/L and is robust to variations in dust extinction. These fits also show that the 10 kpc ring is not just a region of enhanced recent star formation, but is instead a dynamical structure containing a significant overdensity of stars with ages >1 Gyr. (Abridged)Comment: 48 pages including 22 pages of figures. Accepted to the Astrophysical Journal Supplements. Some figures slightly degraded to reduce submission siz

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6x and 30.7x using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3x LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. To highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6x. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near-optimal on the NVIDIA Tesla V100s

Genomic co-processor for long read assembly

Genomics data is transforming medicine and our understanding of life in fundamental ways; however, it is far outpacing Moore's Law. Third-generation sequencing technologies produce 100X longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. In order to enable the vast potential of exponentially growing genomics data, domain specific acceleration provides one of the few remaining approaches to continue to scale compute performance and efficiency, since general-purpose architectures are struggling to handle the huge amount of data needed for genome alignment. The aim of this project is to implement a genomic-coprocessor targeting HPC FPGAs starting from the Darwin FPGA co-processor. In this scenario, the final objective is the simulation and implementation of the algorithms described by Darwin using Alveo boards, exploiting High Bandwidth Memory (HBM) to increase its performance

Threshold dynamic time warping for spatial activity recognition

Non-invasive spatial activity recognition is a difficult task, complicated by variation in how the same activities are conducted and furthermore by noise introduced by video tracking procedures. In this paper we propose an algorithm based on dynamic time warping (DTW) as a viable method with which to quantify segmented spatial activity sequences from a video tracking system. DTW is a widely used technique for optimally aligning or warping temporal sequences through minimisation of the distance between their components. The proposed algorithm threshold DTW (TDTW) is capable of accurate spatial sequence distance quantification and is shown using a three class spatial data set to be more robust and accurate than DTW and the discrete hidden markov model (HMM). We also evaluate the application of a band dynamic programming (DP) constraint to TDTW in order to reduce extraneous warping between sequences and to reduce the computation complexity of the approach. Results show that application of a band DP constraint to TDTW improves runtime performance significantly, whilst still maintaining a high precision and recall

Detecting the orbital character of the spin fluctuation in the Iron-based superconductors with the resonant inelastic X-ray scattering spectroscopy

The orbital distribution of the spin fluctuation in the iron-based superconductors(IBSs) is the key information needed to understand the magnetism, superconductivity and electronic nematicity in these multi-orbital systems. In this work, we propose that the resonant inelastic X-ray scattering(RIXS) technique can be used to probe selectively the spin fluctuation on different Fe $3d$ orbitals. In particular, the spin fluctuation on the three $t_{2g}$ orbitals, namely, the $3d_{xz}$, $3d_{yz}$ and the $3d_{xy}$ orbital, can be selectively probed in the $\sigma\rightarrow\pi'$ scattering geometry by aligning the direction of the outgoing photon in the $y$, $x$ and $z$ direction. Such orbital-resolved information on the spin fluctuation is invaluable for the study of the orbital-selective physics in the IBSs and can greatly advance our understanding on the relation between orbital ordering and spin nematicity in the IBSs and the orbital-selective pairing mechanism in these multi-orbital systems.Comment: 6 pages with new and more informative figures, the explicit form of the RIXS matrix element is provided, and the discussion part has been rewritte