scholarly journals Swarm v2: highly-scalable and high-resolution amplicon clustering

2015 ◽  
Author(s):  
Frédéric Mahé ◽  
Torbjørn Rognes ◽  
Christopher Quince ◽  
Colomban de Vargas ◽  
Micah Dunthorn
Keyword(s):  
High Resolution ◽  
Initial Phase ◽  
Computation Time ◽  
Two Dimensional ◽  
Fine Scale ◽  
Single Linkage ◽  
Fasta Format ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Local Clustering

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2 that has two important novel features: 1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and 2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

scholarly journals Swarm v2: highly-scalable and high-resolution amplicon clustering

2015 ◽  
Author(s):  
Frédéric Mahé ◽  
Torbjørn Rognes ◽  
Christopher Quince ◽  
Colomban de Vargas ◽  
Micah S Dunthorn
Keyword(s):  
High Resolution ◽  
Initial Phase ◽  
Computation Time ◽  
Two Dimensional ◽  
Fine Scale ◽  
Single Linkage ◽  
Fasta Format ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Local Clustering

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2 that has two important novel features: 1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and 2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

scholarly journals Swarm v2: highly-scalable and high-resolution amplicon clustering

2015 ◽  
Author(s):  
Frédéric Mahé ◽  
Torbjørn Rognes ◽  
Christopher Quince ◽  
Colomban de Vargas ◽  
Micah Dunthorn
Keyword(s):  
High Resolution ◽  
Initial Phase ◽  
Computation Time ◽  
Two Dimensional ◽  
Fine Scale ◽  
Single Linkage ◽  
Fasta Format ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Local Clustering

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2 that has two important novel features: 1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and 2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

scholarly journals Swarm v2: highly-scalable and high-resolution amplicon clustering

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1420 ◽  
Author(s):  
Frédéric Mahé ◽  
Torbjørn Rognes ◽  
Christopher Quince ◽  
Colomban de Vargas ◽  
Micah Dunthorn
Keyword(s):  
High Resolution ◽  
Initial Phase ◽  
Computation Time ◽  
Two Dimensional ◽  
Fine Scale ◽  
Single Linkage ◽  
Fasta Format ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Local Clustering

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm ford= 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads withd= 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

High-Resolution, Reflection Mode Tomographic Imaging Part I: Principles and Methods

1989 ◽  
Vol 11 (1) ◽  
pp. 1-21
Author(s):  
A. Herment ◽  
J.P. Guglielmi ◽  
P. Péronneau ◽  
Ph. Dumée
Keyword(s):  
High Resolution ◽  
Image Reconstruction ◽  
Computation Time ◽  
Tomographic Imaging ◽  
Image Resolution ◽  
Square Root ◽  
Two Dimensional ◽  
Reflection Mode ◽  
Reconstruction Process ◽  
General Method

A general method for improving image resolution is derived and applied to ultrasound signals; it combines the principles of both reflection mode tomography and deconvolution. The different possibilities of applying these principles allow two types of approaches to be defined, depending upon whether image reconstruction is achieved on radiofrequency or detected signals. A thorough description of three methods that are of particular interest due to their lower computation costs is presented, and their results quantified. They permit a gain in resolution of the order of ten with respect to two-dimensional deconvolution of images, as well as an improvement of the S/N ratio, which is related to the square root of the number of projections used in the reconstruction process, and a decrease of about four in computation time.

High Resolution Microscopy of Multi-Layered Biological Crystals

1982 ◽  
Vol 40 ◽  
pp. 80-83
Author(s):  
H.A. Cohen ◽  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Low Dose ◽  
Three Dimensional ◽  
Data Interpretation ◽  
Two Dimensional ◽  
Biological Objects ◽  
Density Maps ◽  
Density Map ◽  
Complex Crystal ◽  
High Resolution Microscopy

This tutorial will discuss the methodology of low dose electron diffraction and imaging of crystalline biological objects, the problems of data interpretation for two-dimensional projected density maps of glucose embedded protein crystals, the factors to be considered in combining tilt data from three-dimensional crystals, and finally, the prospects of achieving a high resolution three-dimensional density map of a biological crystal. This methodology will be illustrated using two proteins under investigation in our laboratory, the T4 DNA helix destabilizing protein gp32*I and the crotoxin complex crystal.

High Resolution Stereography of Complementary Freeze-Fracture Replicas Reveals the Presence of Depressions Opposite Membrane Associated Particles of Split Membranes

1971 ◽  
Vol 29 ◽  
pp. 442-443
Author(s):  
Russell L. Steere
Keyword(s):  
High Resolution ◽  
Cardiac Muscle ◽  
Electron Micrographs ◽  
Chromic Acid ◽  
Freeze Fracture ◽  
Distilled Water ◽  
Fine Scale ◽  
Acid Cleaning ◽  
Cleaning Solution

Complementary replicas have revealed the fact that the two common faces observed in electron micrographs of freeze-fracture and freeze-etch specimens are complementary to each other and are thus the new faces of a split membrane rather than the original inner and outer surfaces (1, 2 and personal observations). The big question raised by published electron micrographs is why do we not see depressions in the complementary face opposite membrane-associated particles? Reports have appeared indicating that some depressions do appear but complementarity on such a fine scale has yet to be shown.Dog cardiac muscle was perfused with glutaraldehyde, washed in distilled water, then transferred to 30% glycerol (material furnished by Dr. Joaquim Sommer, Duke Univ., and VA Hospital, Durham, N.C.). Small strips were freeze-fractured in a Denton Vacuum DFE-2 Freeze-Etch Unit with complementary replica tooling. Replicas were cleaned in chromic acid cleaning solution, then washed in 4 changes of distilled water and mounted on opposite sides of the center wire of a Formvar-coated grid.

Tubulin structure at intermediate resolution

1995 ◽  
Vol 53 ◽  
pp. 852-853
Author(s):  
K. H. Downing ◽  
S. G. Wolf ◽  
E. Nogales
Keyword(s):  
High Resolution ◽  
Structural Data ◽  
Therapeutic Drug ◽  
Zinc Ions ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Negative Stain ◽  
Functional Mechanisms ◽  
Tubulin Structure

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.

High resolution two-dimensional motility mapping; Methodology and initial results

2001 ◽  
Vol 120 (5) ◽  
pp. A226-A226 ◽  
Author(s):  
W LAMMERS ◽  
S DHANASEKARAN ◽  
J SLACK ◽  
B STEPHEN
Keyword(s):  
High Resolution ◽  
Two Dimensional ◽  
Initial Results

Diversity of Glycoprotein Deficiencies in Glanzmann’s Thrombasthenia

1985 ◽  
Vol 54 (03) ◽  
pp. 626-629 ◽  
Author(s):  
M Meyer ◽  
F H Herrmann
Keyword(s):  
High Resolution ◽  
Gel Electrophoresis ◽  
Type Ii ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis ◽  
Structural Variant ◽  
Glanzmann’S Thrombasthenia ◽  
Crossed Immunoelectrophoresis ◽  
Glanzmann's Thrombasthenia ◽  
Platelet Proteins

SummaryThe platelet proteins of 9 thrombasthenic patients from 7 families were analysed by high resolution two-dimensional gel electrophoresis (HR-2DE) and crossed immunoelectrophoresis (CIE). In 7 patients both glycoproteins (GPs) IIb and Ilia were absent or reduced to roughly the same extent. In two related patients only a trace of GP Ilb-IIIa complex was detected in CIE, but HR-2DE revealed a glycopeptide in the position of GP Ilia in an amount comparable to type II thrombasthenia. This GP Ilia-like component was neither recognized normally by anti-GP Ilb-IIIa antibodies nor labeled by surface iodination. In unreduced-reduced two-dimensional gel electrophoresis two components were observed in the region of GP Ilia. The assumption of a structural variant of GP Ilia in the two related patients is discussed.

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