Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.

Supplementary data are available at Bioinformatics online.

No abstract

No abstract

We propose a novel end-to-end RGB-D SLAM, iDF-SLAM, which adopts a feature-based deep neural tracker as the front-end and a NeRF-style neural implicit mapper as the back-end. The neural implicit mapper is trained on-the-fly, while though the neural tracker is pretrained on the ScanNet dataset, it is also finetuned along with the training of the neural implicit mapper. Under such a design, our iDF-SLAM is capable of learning to use scene-specific features for camera tracking, thus enabling lifelong learning of the SLAM system. Both the training for the tracker and the mapper are selfsupervised without introducing ground truth poses. We test the performance of our iDF-SLAM on the Replica and ScanNet datasets and compare the results to the two recent NeRF-based neural SLAM systems. The proposed iDF-SLAM demonstrates state-of-the-art results in terms of scene reconstruction and competitive performance in camera tracking.

Background The gene-specific sweep is a selection process where an advantageous mutation along with the nearby neutral sites in a gene region increases the frequency in the population. It has been demonstrated to play important roles in ecological differentiation or phenotypic divergence in microbial populations. Therefore, identifying gene-specific sweeps in microorganisms will not only provide insights into the evolutionary mechanisms, but also unravel potential genetic markers associated with biological phenotypes. However, current methods were mainly developed for detecting selective sweeps in eukaryotic data of sparse genotypes and are not readily applicable to prokaryotic data. Furthermore, some challenges have not been sufficiently addressed by the methods, such as the low spatial resolution of sweep regions and lack of consideration of the spatial distribution of mutations. Results We proposed a novel gene-centric and spatial-aware approach for identifying gene-specific sweeps in prokaryotes and implemented it in a python tool SweepCluster. Our method searches for gene regions with a high level of spatial clustering of pre-selected polymorphisms in genotype datasets assuming a null distribution model of neutral selection. The pre-selection of polymorphisms is based on their genetic signatures, such as elevated population subdivision, excessive linkage disequilibrium, or significant phenotype association. Performance evaluation using simulation data showed that the sensitivity and specificity of the clustering algorithm in SweepCluster is above 90%. The application of SweepCluster in two real datasets from the bacteria Streptococcus pyogenes and Streptococcus suis showed that the impact of pre-selection was dramatic and significantly reduced the uninformative signals. We validated our method using the genotype data from Vibrio cyclitrophicus, the only available dataset of gene-specific sweeps in bacteria, and obtained a concordance rate of 78%. We noted that the concordance rate could be underestimated due to distinct reference genomes and clustering strategies. The application to the human genotype datasets showed that SweepCluster is also applicable to eukaryotic data and is able to recover 80% of a catalog of known sweep regions. Conclusion SweepCluster is applicable to a broad category of datasets. It will be valuable for detecting gene-specific sweeps in diverse genotypic data and provide novel insights on adaptive evolution.

No abstract

Parallel reservoir simulators are now widely used with availability of super computers. Modern massively parallel supercomputers demonstrate great power for simulating large-scale reservoir models. However, improving scalability and efficiency for fully implicit methods on emerging parallel architectures is still challenging. In this paper, we present a robust discretization together with a parallel linear solver algorithm; and we explore the parallel implementation on the world's fastest supercomputer Tianhe-2.Starting with a general compositional model, we focus on the black oil model and developed Parallel eXtension Framework for parallelizing the serial simulator. A parallel preconditioner based on fast auxiliary space preconditioning (FASP) is applied to solve the Jacobian system arising from the fully implicit discretization. The parallel simulator was validated using large-scale black oil benchmark problems, for which parallel scalabilities were tested. Giant reservoir models with over 100 million grid blocks have been simulated within a few minutes, and test the strong scalability of AMG solver with 1 billion unknown. We also demonstrate the parallelization and acceleration using Intel Xeon Phi coprocessors. In the end, the efficiency of the parallel simulator is illustrated by a giant reservoir using up to 10,000 cores, for which the CPU and communication time are summarized for the linear and nonlinear algorithms.