scholarly journals Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment

mSystems ◽  
2021 ◽  
Vol 6 (4) ◽  
Author(s):  
Xiaoquan Su
Keyword(s):  
Beta Diversity ◽  
Quantitative Comparison ◽  
Local Alignment ◽  
Global Alignment ◽  
Community Members ◽  
Ecosystem Properties ◽  
Environmental Features

Quantitative comparison among microbiomes can link microbial beta-diversity to environmental features, thus enabling prediction of ecosystem properties or dissection of host-microbiome interaction. However, to compute beta-diversity, current methods mainly employ the entire community profiles of taxa or functions, which can miss the subtle differences caused by low-abundance community members that may play crucial roles in the properties of interest.

scholarly journals Dig into Multi-modal Cues for Video Retrieval with Hierarchical Alignment

2021 ◽  
Author(s):  
Wenzhe Wang ◽  
Mengdan Zhang ◽  
Runnan Chen ◽  
Guanyu Cai ◽  
Penghao Zhou ◽  
...  
Keyword(s):  
Video Retrieval ◽  
State Of The Art ◽  
Text Retrieval ◽  
Local Alignment ◽  
Global Alignment ◽  
Retrieval Task ◽  
Fine Grained ◽  
Global View ◽  
High Level ◽  
Semantic Correspondence

Multi-modal cues presented in videos are usually beneficial for the challenging video-text retrieval task on internet-scale datasets. Recent video retrieval methods take advantage of multi-modal cues by aggregating them to holistic high-level semantics for matching with text representations in a global view. In contrast to this global alignment, the local alignment of detailed semantics encoded within both multi-modal cues and distinct phrases is still not well conducted. Thus, in this paper, we leverage the hierarchical video-text alignment to fully explore the detailed diverse characteristics in multi-modal cues for fine-grained alignment with local semantics from phrases, as well as to capture a high-level semantic correspondence. Specifically, multi-step attention is learned for progressively comprehensive local alignment and a holistic transformer is utilized to summarize multi-modal cues for global alignment. With hierarchical alignment, our model outperforms state-of-the-art methods on three public video retrieval datasets.

scholarly journals Image Stitching Based on Nonrigid Warping for Urban Scene

Sensors ◽  
2020 ◽  
Vol 20 (24) ◽  
pp. 7050
Author(s):  
Lixia Deng ◽  
Xiuxiao Yuan ◽  
Cailong Deng ◽  
Jun Chen ◽  
Yang Cai
Keyword(s):  
Local Alignment ◽  
Global Alignment ◽  
Image Stitching ◽  
Data Sets ◽  
Function Fitting ◽  
Feature Correspondences ◽  
Urban Scene ◽  
Quantitative Indicators ◽  
Overlapped Region ◽  
Better Than

Image stitching based on a global alignment model is widely used in computer vision. However, the resulting stitched image may look blurry or ghosted due to parallax. To solve this problem, we propose a parallax-tolerant image stitching method based on nonrigid warping in this paper. Given a group of putative feature correspondences between overlapping images, we first use a semiparametric function fitting, which introduces a motion coherence constraint to remove outliers. Then, the input images are warped according to a nonrigid warp model based on Gaussian radial basis functions. The nonrigid warping is a kind of elastic deformation that is flexible and smooth enough to eliminate moderate parallax errors. This leads to high-precision alignment in the overlapped region. For the nonoverlapping region, we use a rigid similarity model to reduce distortion. Through effective transition, the nonrigid warping of the overlapped region and the rigid warping of the nonoverlapping region can be used jointly. Our method can obtain more accurate local alignment while maintaining the overall shape of the image. Experimental results on several challenging data sets for urban scene show that the proposed approach is better than state-of-the-art approaches in both qualitative and quantitative indicators.

scholarly journals The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment

2005 ◽  
Vol 33 (15) ◽  
pp. 4987-4994 ◽  
Author(s):  
S. Sheetlin ◽  
Y. Park ◽  
J. L. Spouge
Keyword(s):  
Local Alignment ◽  
Global Alignment

Human Perceptions and Reflections on the Urban Context

2020 ◽  
pp. 136-155
Author(s):  
Gina S. Lovasi ◽  
Stephen E. Lankenau
Keyword(s):  
Lived Experiences ◽  
Urban Context ◽  
Community Members ◽  
Environmental Features ◽  
Qualitative Approaches ◽  
Human Perceptions ◽  
Ecological Momentary ◽  
Depth Interviews ◽  
Momentary Assessment

To highlight quantitative and qualitative approaches to better understand perceptions and reflections of urban residents relevant to the links between environmental features discussed in Chapter 5 geographically referenced health outcomes discussed in Chapter 7. Strategies to capture what residents perceive, feel, and recommend regarding their environments include characterization of lived experiences (via surveys, focus groups, in depth interviews) as well as detailed assessments of taking place within urban contexts (via ecological momentary assessment, photovoice, ethnography). Participatory approaches that engage community members are illustrated with examples from Bogotá, Madrid, and Philadelphia.

REDUCING THE SEARCH SPACE AND TIME COMPLEXITY OF NEEDLEMAN-WUNSCH ALGORITHM (GLOBAL ALIGNMENT) AND SMITH-WATERMAN ALGORITHM (LOCAL ALIGNMENT) FOR DNA SEQUENCE ALIGNMENT

2015 ◽  
Vol 77 (20) ◽  
Author(s):  
F. N. Muhamad ◽  
R. B. Ahmad ◽  
S. Mohd. Asi ◽  
M. N. Murad
Keyword(s):  
Dynamic Programming ◽  
Dna Sequences ◽  
Sequence Comparison ◽  
Dynamic Programming Algorithm ◽  
Search Space ◽  
Programming Algorithm ◽  
Local Alignment ◽  
Global Alignment ◽  
Main Research ◽  
Dna Sequence Alignment

The fundamental procedure of analyzing sequence content is sequence comparison. Sequence comparison can be defined as the problem of finding which parts of the sequences are similar and which parts are different, namely comparing two sequences to identify similarities and differences between them. A typical approach to solve this problem is to find a good and reasonable alignment between the two sequences. The main research in this project is to align the DNA sequences by using the Needleman-Wunsch algorithm for global alignment and Smith-Waterman algorithm for local alignment based on the Dynamic Programming algorithm. The Dynamic Programming Algorithm is guaranteed to find optimal alignment by exploring all possible alignments and choosing the best through the scoring and traceback techniques. The algorithms proposed and evaluated are to reduce the gaps in aligning sequences as well as the length of the sequences aligned without compromising the quality or correctness of results. In order to verify the accuracy and consistency of measurements obtained in Needleman-Wunsch and Smith-Waterman algorithms the data is compared with Emboss (global) and Emboss (local) with 600 strands test data.

scholarly journals Acceleration of Nucleotide Semi-Global Alignment with Adaptive Banded Dynamic Programming

2017 ◽  
Author(s):  
Hajime Suzuki ◽  
Masahiro Kasahara
Keyword(s):  
Dynamic Programming ◽  
Single Molecule ◽  
Computation Time ◽  
Error Rates ◽  
Nucleotide Sequences ◽  
Sequencing Error ◽  
Local Alignment ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Short Read

AbstractMotivationPairwise alignment of nucleotide sequences has previously been carried out using the seed- and-extend strategy, where we enumerate seeds (shared patterns) between sequences and then extend the seeds by Smith-Waterman-like semi-global dynamic programming to obtain full pairwise alignments. With the advent of massively parallel short read sequencers, algorithms and data structures for efficiently finding seeds have been extensively explored. However, recent advances in single-molecule sequencing technologies have enabled us to obtain millions of reads, each of which is orders of magnitude longer than those output by the short-read sequencers, demanding a faster algorithm for the extension step that accounts for most of the computation time required for pairwise local alignment. Our goal is to design a faster extension algorithm suitable for single-molecule sequencers with high sequencing error rates (e.g., 10-15%) and with more frequent insertions and deletions than substitutions.ResultsWe propose an adaptive banded dynamic programming algorithm for calculating pairwise semi-global alignment of nucleotide sequences that allows a relatively high insertion or deletion rate while keeping band width relatively low (e.g., 32 or 64 cells) regardless of sequence lengths. Our new algorithm eliminated mutual dependences between elements in a vector, allowing an efficient Single-Instruction-Multiple-Data parallelization. We experimentally demonstrate that our algorithm runs approximately 5× faster than the extension alignment algorithm in NCBI BLAST+ while retaining similar sensitivity (recall).We also show that our extension algorithm is more sensitive than the extension alignment routine in DALIGNER, while the computation time is comparable.AvailabilityThe implementation of the algorithm and the benchmarking scripts are available at https://github.com/ocxtal/[email protected]

Paraspinal Muscle Degeneration as an Independent Risk for Loss of Local Alignment in Degenerative Lumbar Scoliosis Patients After Corrective Surgery

2021 ◽  
pp. 219256822110222
Author(s):  
Gengyu Han ◽  
Wei Wang ◽  
Siyu Zhou ◽  
Wei Li ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Paraspinal Muscle ◽  
Local Alignment ◽  
Global Alignment ◽  
Degenerative Lumbar Scoliosis ◽  
Muscle Degeneration ◽  
Corrective Surgery ◽  
Paraspinal Muscles ◽  
Lumbar Scoliosis ◽  
Maintenance Group

Study Design: Retrospective study. Objectives: To investigate the effect of paraspinal muscle degeneration on the maintenance of local and global alignment among degenerative lumbar scoliosis (DLS) patients after corrective surgery. Methods: 98 DLS patients with a mean follow-up period of 38.3 months after corrective surgery were included. The T1 pelvic angle (TPA), lumbar lordosis (LL), pelvic incidence were measured preoperatively, immediate postoperatively and at last follow-up. All patients were divided into LL maintenance group (n = 21) and LL loss group (n = 77). For patients with well-aligned correction (immediate postoperative TPA ≤ 20°, n = 73), they were divided into TPA maintenance group (last follow-up TPA ≤ 20°) and TPA loss group (last follow-up TPA > 20°). The relative gross cross-sectional area (rGCSA) and fat infiltration (FI) of multifidus (MF) and erector spinae (ES), and the relative functional CSA (rFCSA) of psoas major (PS) were measured at L3, L4 and L5 on preoperative magnetic resonance imaging. Results: MF rGCSA were significantly smaller in LL loss group than in LL maintenance group. Both MF rGCSA and PS rFCSA were significantly smaller and MF FI was significantly higher in TPA loss group than in TPA maintenance group. Binary logistic regression revealed that the MF rGCSA was an independent factor of LL loss; Large immediate postoperative TPA was an independent risk factor of TPA loss, but not the parameters of paraspinal muscles. Conclusion: The effect of paraspinal muscles in lower lumbar segments might be mainly focused on the maintenance of local alignment rather than the global alignment.

scholarly journals A survey and evaluations of histogram-based statistics in alignment-free sequence comparison

2017 ◽  
Vol 20 (4) ◽  
pp. 1222-1237 ◽  
Author(s):  
Brian B Luczak ◽  
Benjamin T James ◽  
Hani Z Girgis
Keyword(s):  
Query Sequence ◽  
Sequence Length ◽  
Local Alignment ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Earth Mover’S Distance ◽  
Earth Mover's Distance ◽  
Alignment Free ◽  
Length Difference ◽  
Alignment Algorithms

Abstract Motivation Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. Results We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover’s distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover’s distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours. Availability The source code of the benchmarking tool is available as Supplementary Materials.

Independent and shared effects of environmental features and space driving avian community beta diversity across a coastal gradient in southern Brazil

2013 ◽  
Vol 38 (8) ◽  
pp. 864-873 ◽  
Author(s):  
Andros Tarouco Gianuca ◽  
Vinicius Augusto Galvão Bastazini ◽  
Rafael Antunes Dias ◽  
Malva Isabel Medina Hernández
Keyword(s):  
Beta Diversity ◽  
Southern Brazil ◽  
Avian Community ◽  
Environmental Features

scholarly journals Study of Essential Sequence Analysis Tools in Bioinformatics : A Brief Overview

2021 ◽  
Author(s):  
Ghafran Ali ◽  
Kanza Ashfaq
Keyword(s):  
Nucleic Acid ◽  
Sequence Analysis ◽  
Protein Sequence ◽  
Consensus Sequence ◽  
Local Region ◽  
Local Alignment ◽  
Global Alignment ◽  
Analysis Program ◽  
Entire Duration ◽  
Essential Sequence

Sequence analysis program is outlined that analyzes and investigates homology between various nucleic acid or protein sequence. The dot matrix technique compares the sequences and the consensus sequence is obtained by superimposing on each other all the dot matrices. Local Alignment and Global Alignment both sequence from start to end is the best possible alignment over the entire duration between the two sequences. This method is more important to align with two closely related sequences roughly the same length. This method may not able to generate optimal results for divergent sequences and variable length sequence because between the two sequences it does not recognize very similar local region.

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