Conceptually, we refer the problem as the minimum weight common mutated sequence (MWCMS) problem. The MWCMS model has many applications including multiple sequence alignment problem, the phylogenetic analysis, the DNA sequencing problem, and sequence comparison problem, which encompass a core set of ...
Fourth, the computation of an accurate multiple-sequence alignment is an NP-hard problem, which means that the alignment cannot be solved in a realistic time frame. This situation explains why more than 100 alternative faster methods have been developed over the past three decades [28]. However,...
We present multiple optimizations using single-instruction multiple-data parallelization, efficient cache utilization and a learned index data structure to accelerate the three main computational modules of minimap2: seeding, chaining and pairwise sequence alignment. These optimizations result in an up to ...
Accordingly, we present the development, characterization, and application of a multi-material stereolithography bioprinter that provides controlled material selection, yields precise regional feature alignment, and minimizes bioink mixing. Fluorescent tracers were first used to highlight the broad design ...
SUPPORTED FEATURES Single-end alignment, paired-end alignment • Output in SAM or database-ready binary formats • Multiple GPU implementation MULTI-GPU SUPPORT Yes BarraCUDA Sequence mapping software Alignment of short sequencing reads, alignment of indels with gap openings and extensions. Yes ...
(e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of ...
Multiple Sequence Alignment Based on Set Covers Alexandre H. L. Porto, Valmir C. Barbosa Pages 127-137 A Methodology for Determining Amino-Acid Substitution Matrices from Set Covers Alexandre H. L. Porto, Valmir C. Barbosa Pages 138-148 ...
A Transformer-Based Feature Segmentation and Region Alignment Method For UAV-View Geo-Localization-IEEE 2021-[github] STransFuse: Fusing Swin Transformer and Convolutional Neural Network for Remote Sensing Image Semantic Segmentation-IEEE 2021-[github] ...
2016-11| DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins |Hamid Reza Hassanzadeh, May D. Wang|Arxiv 2016-11| Deep learning with feature embedding for compound-protein interaction prediction |Fangping Wan, Jianyang Zeng|bioRxiv ...
A general RNA sequencing data analysis process involves the quality control of raw data, read alignment and transcript assembly, expression quantification and differential expression analysis (Fig. 4). Fig. 4 Bioinformatics tools commonly used in RNA-seq data analysis. These tools are primarily used ...