Chaotic Ions Motion Optimization (CIMO) for Biological Sequences Local Alignment: COVID-19 as a Case Study

2021 ◽  
pp. 1-8
Author(s):  
Mohamed Issa ◽  
A. M. Helmi ◽  
Mohamed Abd Elaziz ◽  
Siddhartha Bhattacharyya
Keyword(s):  
Local Alignment ◽  
Biological Sequences ◽  
Motion Optimization

scholarly journals BASiNET—BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification

2018 ◽  
Vol 46 (16) ◽  
pp. e96-e96 ◽  
Author(s):  
Eric Augusto Ito ◽  
Isaque Katahira ◽  
Fábio Fernandes da Rocha Vicente ◽  
Luiz Filipe Protasio Pereira ◽  
Fabrício Martins Lopes
Keyword(s):  
Biological Sequences ◽  
Non Coding Rnas

scholarly journals High speed BLASTN: an accelerated MegaBLAST search tool

2015 ◽  
Vol 43 (16) ◽  
pp. 7762-7768 ◽  
Author(s):  
Ying Chen ◽  
Weicai Ye ◽  
Yongdong Zhang ◽  
Yuesheng Xu
Keyword(s):  
Sequence Alignment ◽  
High Speed ◽  
Lookup Table ◽  
Local Alignment ◽  
Biological Sequences ◽  
Parallel Performance ◽  
Seeding Method ◽  
Computational Speed ◽  
Search Tool ◽  
Nucleotide Database

Abstract 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.

scholarly journals Detecting Source Code Plagiarism on .NET Programming Languages using Low-level Representation and Adaptive Local Alignment

2017 ◽  
Vol 41 (1) ◽  
pp. 105-123 ◽  
Author(s):  
Faqih Salban Rabbani ◽  
Oscar Karnalim
Keyword(s):  
Programming Languages ◽  
State Of The Art ◽  
Source Code ◽  
Point Of View ◽  
Local Alignment ◽  
Plagiarism Detection ◽  
Low Level ◽  
Intermediate Language ◽  
Token Sequence

Even though there are various source code plagiarism detection approaches, only a few works which are focused on low-level representation for deducting similarity. Most of them are only focused on lexical token sequence extracted from source code. In our point of view, low-level representation is more beneficial than lexical token since its form is more compact than the source code itself. It only considers semantic-preserving instructions and ignores many source code delimiter tokens. This paper proposes a source code plagiarism detection which rely on low-level representation. For a case study, we focus our work on .NET programming languages with Common Intermediate Language as its low-level representation. In addition, we also incorporate Adaptive Local Alignment for detecting similarity. According to Lim et al, this algorithm outperforms code similarity state-of-the-art algorithm (i.e. Greedy String Tiling) in term of effectiveness. According to our evaluation which involves various plagiarism attacks, our approach is more effective and efficient when compared with standard lexical-token approach. 

The Genesis and Internal Dynamics of El Salvador's People's Revolutionary Army, 1970–1976

2014 ◽  
Vol 38 (01) ◽  
pp. 102-129
Author(s):  
ALBERTO MARTÍN ÁLVAREZ ◽  
EUDALD CORTINA ORERO
Keyword(s):  
Latin America ◽  
El Salvador ◽  
Early Years ◽  
Left Wing ◽  
Internal Dynamics ◽  
Internal Coherence ◽  
The 1960S

AbstractUsing interviews with former militants and previously unpublished documents, this article traces the genesis and internal dynamics of the Ejército Revolucionario del Pueblo (People's Revolutionary Army, ERP) in El Salvador during the early years of its existence (1970–6). This period was marked by the inability of the ERP to maintain internal coherence or any consensus on revolutionary strategy, which led to a series of splits and internal fights over control of the organisation. The evidence marshalled in this case study sheds new light on the origins of the armed Salvadorean Left and thus contributes to a wider understanding of the processes of formation and internal dynamics of armed left-wing groups that emerged from the 1960s onwards in Latin America.

Culture and the plasticity of perception

2020 ◽  
Vol 43 ◽  
Author(s):  
Michael Lifshitz ◽  
T. M. Luhrmann
Keyword(s):  
Cultural Context ◽  
Sensory Experience ◽  
Cultural Learning ◽  
The World

Abstract Culture shapes our basic sensory experience of the world. This is particularly striking in the study of religion and psychosis, where we and others have shown that cultural context determines both the structure and content of hallucination-like events. The cultural shaping of hallucinations may provide a rich case-study for linking cultural learning with emerging prediction-based models of perception.

Dual systems for all: Higher-order, role-based relational reasoning as a uniquely derived feature of human cognition

2019 ◽  
Vol 42 ◽  
Author(s):  
Daniel J. Povinelli ◽  
Gabrielle C. Glorioso ◽  
Shannon L. Kuznar ◽  
Mateja Pavlic
Keyword(s):  
Temporal Reasoning ◽  
Higher Order ◽  
Important Case ◽  
Human Cognition ◽  
Relational Reasoning ◽  
Dual Systems ◽  
First Order ◽  
Reasoning System ◽  
Role Based

Abstract Hoerl and McCormack demonstrate that although animals possess a sophisticated temporal updating system, there is no evidence that they also possess a temporal reasoning system. This important case study is directly related to the broader claim that although animals are manifestly capable of first-order (perceptually-based) relational reasoning, they lack the capacity for higher-order, role-based relational reasoning. We argue this distinction applies to all domains of cognition.

Sociocultural memory development research drives new directions in gadgetry science

2019 ◽  
Vol 42 ◽  
Author(s):  
Penny Van Bergen ◽  
John Sutton
Keyword(s):  
Episodic Memory ◽  
Autobiographical Memory ◽  
Developmental Psychology ◽  
Cross Cultural ◽  
Memory Development ◽  
Development Research ◽  
Cultural Research ◽  
New Directions ◽  
Cross Cultural Research

Abstract Sociocultural developmental psychology can drive new directions in gadgetry science. We use autobiographical memory, a compound capacity incorporating episodic memory, as a case study. Autobiographical memory emerges late in development, supported by interactions with parents. Intervention research highlights the causal influence of these interactions, whereas cross-cultural research demonstrates culturally determined diversity. Different patterns of inheritance are discussed.

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