scholarly journals Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points

2018 ◽  
Vol 35 (2) ◽  
pp. 211-218 ◽  
Author(s):  
Chris-André Leimeister ◽  
Thomas Dencker ◽  
Burkhard Morgenstern
Keyword(s):  
Multiple Alignment ◽  
Related Genome ◽  
Genome Sequences ◽  
Anchor Points

scholarly journals benchNGS : An approach to benchmark short reads alignment tools

2015 ◽  
Author(s):  
Farzana Rahman ◽  
Mehedi Hassan ◽  
Alona Kryshchenko ◽  
Inna Dubchak ◽  
Tatiana V Tatarinova ◽  
...  
Keyword(s):  
Reference Genome ◽  
Global Alignment ◽  
Short Report ◽  
Related Genome ◽  
Genome Sequences ◽  
Short Reads ◽  
Relevant Reference ◽  
Next Generation Sequencing Ngs ◽  
Reference Genomes ◽  
Generation Sequencing

In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance. We propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools .

SNV Reoccurrence in Multiple Regions in the Genome of 2019-nCoV

2020 ◽  
Author(s):  
Xinjun He ◽  
Wei Yue ◽  
Jun Yan
Keyword(s):  
Rapid Development ◽  
Rapid Evolution ◽  
Health Concern ◽  
Related Genome ◽  
Public Health Concern ◽  
Genome Sequences ◽  
Viral Recombination ◽  
Multiple Regions ◽  
Different Strains ◽  
Fast Transmission

The rapid development of 2019-2020 Wuhan seafood market pneumonia currently posed a major public health concern in China. Genome sequencing identified a novel beta-coronavirus closely related to SARS-CoV, named 2019-nCoV by WHO, as the cause of this pandemic disease. Viruses with single stranded RNA genome are prone to evolve quickly by accumulation of mutations, such as SNV, INDEL and cross viral recombination, aiding fast transmission among hosts and cross species. Here we collected related genome sequences and investigated variations shared by different strains of 2019-nCoV, identified reoccurrence of SNV mutations in clusters of patients, an indication of rapid evolution of 2019-nCoV at the transmission from animal host to human. The information collected herein would help to understand the dynamics of current pandemic.

scholarly journals SNV Reoccurrence in Multiple Regions in the Genome of 2019-nCoV

2020 ◽  
Author(s):  
Xinjun He ◽  
Wei Yue ◽  
Jun Yan
Keyword(s):  
Rapid Development ◽  
Rapid Evolution ◽  
Health Concern ◽  
Related Genome ◽  
Public Health Concern ◽  
Genome Sequences ◽  
Viral Recombination ◽  
Multiple Regions ◽  
Different Strains ◽  
Fast Transmission

The rapid development of 2019-2020 Wuhan seafood market pneumonia currently posed a major public health concern in China. Genome sequencing identified a novel beta-coronavirus closely related to SARS-CoV, named 2019-nCoV by WHO, as the cause of this pandemic disease. Viruses with single stranded RNA genome are prone to evolve quickly by accumulation of mutations, such as SNV, INDEL and cross viral recombination, aiding fast transmission among hosts and cross species. Here we collected related genome sequences and investigated variations shared by different strains of 2019-nCoV, identified reoccurrence of SNV mutations in clusters of patients, an indication of rapid evolution of 2019-nCoV at the transmission from animal host to human. The information collected herein would help to understand the dynamics of current pandemic.

scholarly journals benchNGS : An approach to benchmark short reads alignment tools

2015 ◽  
Author(s):  
Farzana Rahman ◽  
Mehedi Hassan ◽  
Alona Martin Kryshchenko ◽  
Inna Dubchak ◽  
Nikolai Nickolai Alexandrov ◽  
...  
Keyword(s):  
Reference Genome ◽  
Global Alignment ◽  
Short Report ◽  
Related Genome ◽  
Genome Sequences ◽  
Short Reads ◽  
Relevant Reference ◽  
Next Generation Sequencing Ngs ◽  
Reference Genomes ◽  
Generation Sequencing

In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance. We propose a benchmark to assess accuracy of the short reads mapping based on the precomputed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools.

scholarly journals benchNGS : An approach to benchmark short reads alignment tools

2015 ◽  
Author(s):  
Farzana Rahman ◽  
Mehedi Hassan ◽  
Alona Kryshchenko ◽  
Inna Dubchak ◽  
Tatiana V Tatarinova ◽  
...  
Keyword(s):  
Reference Genome ◽  
Global Alignment ◽  
Short Report ◽  
Related Genome ◽  
Genome Sequences ◽  
Short Reads ◽  
Relevant Reference ◽  
Next Generation Sequencing Ngs ◽  
Reference Genomes ◽  
Generation Sequencing

In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance. We propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools .

A Heuristic Method Based on Multi-Objective Optimization Concept for Solving RNA Multiple Alignment

2017 ◽  
Vol 10 (5) ◽  
pp. 371
Author(s):  
Arakil Chentoufi ◽  
Abdelhakim El Fatmi ◽  
Molay Ali Bekri ◽  
Said Benhlima ◽  
Mohamed Sabbane
Keyword(s):  
Heuristic Method ◽  
Multiple Alignment ◽  
Multi Objective Optimization ◽  
Multi Objective

The Development of the Mental Representation of Numbers 0-10 in Elementary School Children

2020 ◽  
Author(s):  
Anat Feldman ◽  
Michael Shmueli ◽  
Dror Dotan ◽  
Joseph Tzelgov ◽  
Andrea Berger
Keyword(s):  
Sixth Grade ◽  
Number Line ◽  
Number Representation ◽  
Large Numbers ◽  
Position Task ◽  
Sigmoidal Curve ◽  
Anchor Points ◽  
The Right ◽  
Line P ◽  
Best Fit

In recent years, there has been growing interest in the development of mental number line (MNL) representation examined using a number-to-position task. In the present study, we investigated the development of number representation on a 0-10 number line using a computerized version of the number-to-position task on a touchscreen, with restricted response time; 181 children from first through sixth grade were tested. We found that the pattern of estimated number position on the physical number line was best fit by the sigmoidal curve function–which was characterized by underestimation of small numbers and overestimation of large numbers–and that the breakpoint changed with age. Moreover, we found that significant developmental leaps in MNL representation occurred between the first and second grades and again between the second and third grades, which was reflected in the establishment of the right endpoint and the number 5 as anchor points, yielding a more accurate placement of other numbers along the number line.

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