scholarly journals Using cluster edge counting to aggregate iterations of centroid-linkage clustering results and avoid large distance matrices

2017 ◽  
Vol 4 (1) ◽  
pp. e68
Author(s):  
Matthew Kellom ◽  
Jason Raymond
Keyword(s):  
High Throughput Sequencing ◽  
Low Frequency ◽  
Basic Research ◽  
Distance Matrix ◽  
Personal Computers ◽  
Specific Sequence ◽  
Cluster Accuracy ◽  
Distance Matrices ◽  
Edge List ◽  
Memory Resources

Sequence clustering is a fundamental tool of molecular biology that is being challenged by increasing dataset sizes from high-throughput sequencing. The agglomerative algorithms that have been relied upon for their accuracy require the construction of computationally costly distance matrices which can overwhelm basic research personal computers. Alternative algorithms exist, such as centroid-linkage, to circumvent large memory requirements but their results are often input-order dependent. We present a method for bootstrapping the results of many centroid-linkage clustering iterations into an aggregate set of clusters, increasing cluster accuracy without a distance matrix. This method ranks cluster edges by conservation across iterations and reconstructs aggregate clusters from the resulting ranked edge list, pruning out low-frequency cluster edges that may have been a result of a specific sequence input order. Aggregating centroid-linkage clustering iterations can help researchers using basic research personal computers acquire more reliable clustering results without increasing memory resources.

scholarly journals Identifying and Tracking Low-Frequency Virus-Specific TCR Clonotypes Using High-Throughput Sequencing

Cell Reports ◽  
2018 ◽  
Vol 25 (9) ◽  
pp. 2369-2378.e4 ◽  
Author(s):  
Kyle Wolf ◽  
Tyler Hether ◽  
Pavlo Gilchuk ◽  
Amrendra Kumar ◽  
Ahmad Rajeh ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Low Frequency

scholarly journals Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments

2021 ◽  
Author(s):  
Brian P. Anton ◽  
Alexey Fomenkov ◽  
Victoria Wu ◽  
Richard J. Roberts
Keyword(s):  
Single Molecule ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Specific Sequence ◽  
Genome Wide ◽  
Cost Effective Alternative ◽  
Simple Column ◽  
Sequencing Platforms

ABSTRACTSingle-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that “write” these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

scholarly journals Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0247541
Author(s):  
Brian P. Anton ◽  
Alexey Fomenkov ◽  
Victoria Wu ◽  
Richard J. Roberts
Keyword(s):  
Single Molecule ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Specific Sequence ◽  
Genome Wide ◽  
Cost Effective Alternative ◽  
Simple Column ◽  
Sequencing Platforms

Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that “write” these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

scholarly journals The significance of Gerta Vrbová's low-frequency stimulation experiment

2021 ◽  
Author(s):  
Dirk Pette
Keyword(s):  
Low Frequency ◽  
Basic Research ◽  
Contractile Properties ◽  
Scientific Cooperation ◽  
Low Frequency Stimulation ◽  
Slow Twitch Muscle ◽  
Frequency Stimulation ◽  
Time Courses ◽  
Fast Twitch

An inspiring scientific cooperation has come to an end, when Gerta Vrbová, an internationally renowned researcher in the field of neuromuscular interactions, passed away on October 2, 2020. Comparative EMG studies had led Gerta to suggest that different contractile properties of fast- and slow-twitch muscle fibers relate to specific firing patterns of their motoneurones. In support of her hypothesis, long term stimulation of fast-twitch muscles with a stimulus pattern resembling that of slow motoneurones, were shown to induce a pronounced fast-to-slow shift in contractile properties. In our cooperation which started in 1970, and also in cooperation with others, Gerta's experiment proved to be an ideal model for the study of neurally controlled changes in phenotype characteristics at various levels of molecular and cellular organization, their time courses and ranges. It has become most important in basic research on the adaptive potential or plasticity of muscle.

A DIMENSIONLESS FIT MEASURE FOR PHYLOGENETIC DISTANCE TREES

2005 ◽  
Vol 03 (06) ◽  
pp. 1429-1440 ◽  
Author(s):  
MANUEL GIL ◽  
CHRISTOPHE DESSIMOZ ◽  
GASTON H. GONNET
Keyword(s):  
Phylogenetic Trees ◽  
Distance Matrix ◽  
Phylogenetic Distance ◽  
Linear Transformations ◽  
Relative Measure ◽  
Absolute Measure ◽  
Distance Matrices ◽  
Fit Index

We present a dimensionless fit index for phylogenetic trees that have been constructed from distance matrices. It is designed to measure the quality of the fit of the data to a tree in absolute terms, independent of linear transformations on the distance matrix. The index can be used as an absolute measure to evaluate how well a set of data fits to a tree, or as a relative measure to compare different methods that are expected to produce the same tree. The usefulness of the index is demonstrated in three examples.

Nondestructive Damage Detection of Bridges: A Status Review

2001 ◽  
Vol 4 (2) ◽  
pp. 75-91 ◽  
Author(s):  
Xiaotong Wang ◽  
Chih-Chen Chang ◽  
Lichu Fan
Keyword(s):  
Damage Detection ◽  
Rapid Development ◽  
Low Frequency ◽  
Basic Research ◽  
Digital Signal ◽  
Point Of View ◽  
Detection Methods ◽  
Measured Signal ◽  
Destructive Testing ◽  
Bridge Damage

The recent advances in detecting and locating damage in bridges by different kinds of non-destructive testing and evaluation (NDT&E) methods are reviewed. From the application point of view, classifications for general bridge components and their damage types are presented. The relationships between damage, bridge components, and NDT&E techniques are summarized. Many useful WEB sources of NDT&E techniques in bridge damage detection are given. It is concluded that: (1) vibration-based damage detection methods are successful to a certain extent, especially when the overall damage is significant and, low frequency vibration can identify those areas where more detailed local inspection should be concentrated; (2) robust identification techniques that are able to locate damage based on realistic measured data sets still seem a long way from reality, and, basic research is still necessary in the mean time; (3) the rapid development of computer technology and digital signal processing (DSP) techniques greatly impacts upon the conventional NDT techniques, especially in control data processing and data displaying, as well as in simulation and modeling; (4) most of the NDT&E techniques introduced in this paper have their own practical commercial systems, but the effort required for combining the theoretical, experimental and engineering achievements, is still a challenging task when establishing the relationship between the unknown quantities and the measured signal parameters and specialised instruments have shown great advantages for doing some things more effectively than general ones; (5) in bridge damage detection, a problem usually requires the application of different NDT&E techniques; two or more independent techniques are needed to enable confidence in the results.

CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning

2020 ◽  
Vol 36 (11) ◽  
pp. 3385-3392
Author(s):  
Zi-Lin Liu ◽  
Jing-Hao Hu ◽  
Fan Jiang ◽  
Yun-Dong Wu
Keyword(s):  
Machine Learning ◽  
Sequence Alignment ◽  
Structure Prediction ◽  
High Throughput Sequencing ◽  
Prediction Method ◽  
General Purpose ◽  
Supplementary Information ◽  
Model Quality ◽  
Specific Sequence ◽  
Structure Information

Abstract Motivation High-throughput sequencing discovers many naturally occurring disulfide-rich peptides or cystine-rich peptides (CRPs) with diversified bioactivities. However, their structure information, which is very important to peptide drug discovery, is still very limited. Results We have developed a CRP-specific structure prediction method called Cystine-Rich peptide Structure Prediction (CRiSP), based on a customized template database with cystine-specific sequence alignment and three machine-learning predictors. The modeling accuracy is significantly better than several popular general-purpose structure modeling methods, and our CRiSP can provide useful model quality estimations. Availability and implementation The CRiSP server is freely available on the website at http://wulab.com.cn/CRISP. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SCEDS: protein fragments for molecular replacement inPhaser

2013 ◽  
Vol 69 (11) ◽  
pp. 2216-2225 ◽  
Author(s):  
Airlie J. McCoy ◽  
Robert A. Nicholls ◽  
Thomas R. Schneider
Keyword(s):  
Normal Modes ◽  
Low Frequency ◽  
Distance Matrix ◽  
Triaxial Ellipsoid ◽  
Molecular Replacement ◽  
Elastic Network Model ◽  
Protein Fragments ◽  
Template Model ◽  
Invariant Regions ◽  
The Difference

A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of Cαatoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lowerRfactor after ten cycles of all-atom refinement withREFMAC5 than the original template structure. The method has been implemented in the softwarePhaser.

Sea Motion Simulation, Very Low Frequency Vibration, and Motion Sickness

1976 ◽  
Vol 20 (20) ◽  
pp. 462-462
Author(s):  
Michael E. McCauley
Keyword(s):  
Motion Sickness ◽  
Degrees Of Freedom ◽  
Low Frequency ◽  
Vertical Motion ◽  
Basic Research ◽  
Future Research ◽  
Naval Research ◽  
Low Frequency Vibration ◽  
Office Of Naval Research ◽  
Linear Oscillation

The office of Naval Research/Human Factors Research (ONR/HFR) Motion Generator was designed with three degrees of freedom (heave, pitch, and roll) to simulate the motion of an air-sea craft in varying ocean conditions through Sea State 5. Recent upgrading of the device has provided the capability for simulating the motion of advanced design sea craft as well as certain aspects of vertical motion common to land, sea, and air vehicles. Since 1968, the simulator has been used for investigation of the following topics: (1) basic research to provide equations for the prediction of motion sickness incidence based on parameters of vertical linear oscillation, (2) crew performance during simulated motion of two types of proposed naval vessels, and (3) evaluation of the efficacy of antimotion sickness medications in alleviating the symptoms of motion sickness. This simulator provides the opportunity for future research on the effects of motion on physiological and psychological processes as well as task performance.

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