scholarly journals On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

2014 ◽  
pp. 183-195 ◽  
Author(s):  
Giuseppe Narzisi ◽  
Bud Mishra ◽  
Michael C. Schatz
Keyword(s):  
Sequence Assembly ◽  
Algorithmic Complexity ◽  
Assembly Problem

A Roadmap to Sequence Assembly Evaluation Tools

2020 ◽  
Vol 15 ◽  
Author(s):  
Sara El-Metwally ◽  
Eslam Hamouda ◽  
Mayada Tarek
Keyword(s):  
Data Analysis ◽  
Evaluation Process ◽  
Sequence Assembly ◽  
Assessment Tools ◽  
Accurate Information ◽  
End User ◽  
Evaluation Tools ◽  
Assembly Evaluation ◽  
Assembly Pipeline ◽  
Evaluation Approaches

: The assembly evaluation process is the starting step towards meaningful downstream data analysis. We need to know how much accurate information is included in an assembled sequence before going further to any data analysis stage. Four basic metrics are targeted by different assembly evaluation tools: contiguity, accuracy, completeness, and contamination. Some tools evaluate these metrics based on comparing the assembly results to a closely related reference. Others utilize different types of heuristics to overcome the missing of a guiding reference, such as the consistency between assembly results and sequencing reads. In this paper, we discuss the assembly evaluation process as a core stage in any sequence assembly pipeline and present a roadmap that is followed by most assembly evaluation tools to assess different metrics. We highlight the challenges that currently exist in the assembly evaluation tools and summarize their technical and practical details to help the end-users choose the best tool according to their working scenarios. To address the similarities/differences among different assembly assessment tools, including their evaluation approaches, metrics, comprehensive nature, limitations, usability and how the evaluated results are presented to the end-user, we provide a practical example for evaluating Velvet assembly results for S. aureus dataset from GAGE competition. A Github repository (https://github.com/SaraEl-Metwally/Assembly-Evaluation-Tools) is created for evaluation result details along with their generated command line parameters.

scholarly journals The algorithmic complexity of mixed domination in graphs

2011 ◽  
Vol 412 (22) ◽  
pp. 2387-2392 ◽  
Author(s):  
Yancai Zhao ◽  
Liying Kang ◽  
Moo Young Sohn
Keyword(s):  
Algorithmic Complexity ◽  
Domination In Graphs

scholarly journals Single Chain Mean-Field Theory Study on Responsive Behavior of Semiflexible Polymer Brush

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 778
Author(s):  
Yingli Niu ◽  
Xiangyu Bu ◽  
Xinghua Zhang
Keyword(s):  
Field Theory ◽  
Message Passing Interface ◽  
Mean Field Theory ◽  
Mean Field ◽  
Algorithmic Complexity ◽  
Ensemble Average ◽  
Single Chain ◽  
Metropolis Monte Carlo ◽  
Rigid Rod ◽  
Chain Conformations

The application of single chain mean-field theory (SCMFT) on semiflexible chain brushes is reviewed. The worm-like chain (WLC) model is the best mode of semiflexible chain that can continuously recover to the rigid rod model and Gaussian chain (GC) model in rigid and flexible limits, respectively. Compared with the commonly used GC model, SCMFT is more applicable to the WLC model because the algorithmic complexity of the WLC model is much higher than that of the GC model in self-consistent field theory (SCFT). On the contrary, the algorithmic complexity of both models in SCMFT are comparable. In SCMFT, the ensemble average of quantities is obtained by sampling the conformations of a single chain or multi-chains in the external auxiliary field instead of solving the modified diffuse equation (MDE) in SCFT. The precision of this calculation is controlled by the number of bonds Nm used to discretize the chain contour length L and the number of conformations M used in the ensemble average. The latter factor can be well controlled by metropolis Monte Carlo simulation. This approach can be easily generalized to solve problems with complex boundary conditions or in high-dimensional systems, which were once nightmares when solving MDEs in SCFT. Moreover, the calculations in SCMFT mainly relate to the assemble averages of chain conformations, for which a portion of conformations can be performed parallel on different computing cores using a message-passing interface (MPI).

scholarly journals Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 518
Author(s):  
Zequn Chen ◽  
Xiwu Qi ◽  
Xu Yu ◽  
Ying Zheng ◽  
Zhiqi Liu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Essential Oils ◽  
Gene Family ◽  
Genome Sequence ◽  
Sequence Assembly ◽  
Terpene Synthase ◽  
Genome Sequence Assembly ◽  
Mentha Longifolia ◽  
Specific Expansion ◽  
Species Specific

Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.

scholarly journals Algorithmic complexity of recursive and inductive algorithms

2004 ◽  
Vol 317 (1-3) ◽  
pp. 31-60 ◽  
Author(s):  
Mark Burgin
Keyword(s):  
Algorithmic Complexity

Fixed-parameter tractability for the tree assembly problem

2021 ◽  
Author(s):  
Feng Shi ◽  
Jie You ◽  
Zhen Zhang ◽  
Jingyi Liu ◽  
Jianxin Wang
Keyword(s):  
Fixed Parameter Tractability ◽  
Fixed Parameter ◽  
Assembly Problem

Push-Pull Pair of Single Action Mechanisms to Preload Strut and Node Joints in the Robotic Assembly of Structures in Space

1992 ◽  
Author(s):  
W. V. Brewer
Keyword(s):  
Separation Distance ◽  
Variable Length ◽  
Superior Performance ◽  
Robotic Assembly ◽  
Design Specification ◽  
Single Action ◽  
Action Mechanisms ◽  
Reference Length ◽  
Crucial Problem ◽  
Assembly Problem

Abstract When strut and node components are used for truss construction or repair, an assembly problem occurs if a strut must fit between nodes whose separation distance is either more or less than the design specification. In such circumstances two actions would permit continued assembly: 1. Change strut length 2. Move the nodes. Variable length struts fit between nodes and (or) move them. They are preloaded at the joint against a reference length in an attempt to maintain the desired dimension. As a by-product they either pull the nodes together or push them apart. Most cannot do both, and are therefore characterized as “single action”; those that can do both are “double action”. Double action mechanisms are currently being used for robotic truss assembly because they solve the above stated crucial problem in both directions. Single action mechanisms tend to exhibit superior performance in all other categories. They benefit from the attributes that accompany their simplicity. The titled concept combines the major advantage of double action with the simplicity of single action. This is demonstrated with an example.

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