Sequence homology detection through large scale pattern discovery

1999 ◽  
Author(s):  
Aris Floratos ◽  
Isidore Rigoutsos ◽  
Laxmi Parida ◽  
Gustova Stolovitzky ◽  
Yuan Gao
Keyword(s):  
Sequence Homology ◽  
Large Scale ◽  
Pattern Discovery ◽  
Homology Detection

scholarly journals Synaptonemal Complex dimerization regulates chromosome alignment and crossover patterning in meiosis

2020 ◽  
Author(s):  
Spencer G. Gordon ◽  
Lisa E. Kursel ◽  
Kewei Xu ◽  
Ofer Rog
Keyword(s):  
Synaptonemal Complex ◽  
Sequence Homology ◽  
Genetic Information ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Homologous Chromosomes ◽  
C Elegans ◽  
Local Sequence ◽  
Chromosome Alignment ◽  
Dimerization Interface

AbstractDuring sexual reproduction the parental homologous chromosomes find each other (pair) and align along their lengths by integrating local sequence homology with large-scale contiguity, thereby allowing for precise exchange of genetic information. The Synaptonemal Complex (SC) is a conserved zipper-like structure that assembles between the homologous chromosomes. This phase-separated interface brings chromosomes together and regulates exchanges between them. However, the molecular mechanisms by which the SC carries out these functions remain poorly understood. Here we isolated and characterized two mutations in the dimerization interface in the middle of the SC zipper in C. elegans. The mutations perturb both chromosome alignment and the regulation of genetic exchanges. Underlying the chromosome-scale phenotypes are distinct alterations to the way SC subunits interact with one another. We propose that the SC brings homologous chromosomes together through two biophysical activities: obligate dimerization that prevents assembly on unpaired chromosomes; and a tendency to phase-separate that extends pairing interactions along the entire length of the chromosomes.

Global Sequence Homology Detection Using Word Conservation Probability

2011 ◽  
Vol 3 (4) ◽  
pp. 1-9
Author(s):  
Dae-Kyum Kim ◽  
Jae-Seong Yang ◽  
Jinho Kim ◽  
Sanguk Kim
Keyword(s):  
Sequence Homology ◽  
Homology Detection

scholarly journals Synaptonemal Complex dimerization regulates chromosome alignment and crossover patterning in meiosis

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009205
Author(s):  
Spencer G. Gordon ◽  
Lisa E. Kursel ◽  
Kewei Xu ◽  
Ofer Rog
Keyword(s):  
Sexual Reproduction ◽  
Synaptonemal Complex ◽  
Sequence Homology ◽  
Genetic Information ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Homologous Chromosomes ◽  
Local Sequence ◽  
Chromosome Alignment ◽  
Dimerization Interface

During sexual reproduction the parental homologous chromosomes find each other (pair) and align along their lengths by integrating local sequence homology with large-scale contiguity, thereby allowing for precise exchange of genetic information. The Synaptonemal Complex (SC) is a conserved zipper-like structure that assembles between the homologous chromosomes, bringing them together and regulating exchanges between them. However, the molecular mechanisms by which the SC carries out these functions remain poorly understood. Here we isolated and characterized two mutations in the dimerization interface in the middle of the SC zipper in C. elegans. The mutations perturb both chromosome alignment and the regulation of genetic exchanges. Underlying the chromosome-scale phenotypes are distinct alterations to the way SC subunits interact with one another. We propose a model whereby the SC brings homologous chromosomes together through two activities: obligate zipping that prevents assembly on unpaired chromosomes; and a tendency to extend pairing interactions along the entire length of the chromosomes.

PCPD: A Parallel Crime Pattern Discovery System for Large-Scale Spatiotemporal Data Based on Fuzzy Clustering

2019 ◽  
Vol 21 (6) ◽  
pp. 1961-1974 ◽  
Author(s):  
Khin Nandar Win ◽  
Jianguo Chen ◽  
Yuedan Chen ◽  
Philippe Fournier-Viger
Keyword(s):  
Fuzzy Clustering ◽  
Large Scale ◽  
Pattern Discovery ◽  
Spatiotemporal Data ◽  
Discovery System ◽  
Crime Pattern

scholarly journals A work stealing based approach for enabling scalable optimal sequence homology detection

2015 ◽  
Vol 79-80 ◽  
pp. 132-142 ◽  
Author(s):  
Jeff Daily ◽  
Ananth Kalyanaraman ◽  
Sriram Krishnamoorthy ◽  
Abhinav Vishnu
Keyword(s):  
Sequence Homology ◽  
Homology Detection ◽  
Work Stealing ◽  
Optimal Sequence

scholarly journals Shrinkage observed-to-expected ratios for robust and transparent large-scale pattern discovery

2011 ◽  
Vol 22 (1) ◽  
pp. 57-69 ◽  
Author(s):  
G Niklas Norén ◽  
Johan Hopstadius ◽  
Andrew Bate
Keyword(s):  
Observational Data ◽  
Large Scale ◽  
Statistical Significance ◽  
Pattern Discovery ◽  
Null Model ◽  
Improve Patient Care ◽  
Data Sets ◽  
Practical Relevance ◽  
Random Fluctuations ◽  
Event Rates

Large observational data sets are a great asset to better understand the effects of medicines in clinical practice and, ultimately, improve patient care. For an empirical pattern in observational data to be of practical relevance, it should represent a substantial deviation from the null model. For the purpose of identifying such deviations, statistical significance tests are inadequate, as they do not on their own distinguish the magnitude of an effect from its data support. The observed-to-expected (OE) ratio on the other hand directly measures strength of association and is an intuitive basis to identify a range of patterns related to event rates, including pairwise associations, higher order interactions and temporal associations between events over time. It is sensitive to random fluctuations for rare events with low expected counts but statistical shrinkage can protect against spurious associations. Shrinkage OE ratios provide a simple but powerful framework for large-scale pattern discovery. In this article, we outline a range of patterns that are naturally viewed in terms of OE ratios and propose a straightforward and effective statistical shrinkage transformation that can be applied to any such ratio. The proposed approach retains emphasis on the practical relevance and transparency of highlighted patterns, while protecting against spurious associations.

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