scholarly journals Evolutionary Sequence Analysis and Visualization with Wasabi

2020 ◽  
pp. 225-240
Author(s):  
Andres Veidenberg ◽  
Ari Löytynoja
Keyword(s):  
Sequence Analysis ◽  
Evolutionary Sequence

scholarly journals Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

2016 ◽  
Author(s):  
Duccio Malinverni ◽  
Alfredo Jost Lopez ◽  
Paolo De Los Rios ◽  
Gerhard Hummer ◽  
Alessandro Barducci
Keyword(s):  
Sequence Analysis ◽  
Structural Model ◽  
Molecular Simulations ◽  
Evolutionary Sequence ◽  
Multi Scale ◽  
Atomistic Models ◽  
Structural Details ◽  
Shock Proteins ◽  
Interaction Surface ◽  
Shed Light

AbstractThe interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.

scholarly journals Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

2015 ◽  
Vol 33 (4) ◽  
pp. 1126-1130 ◽  
Author(s):  
Andres Veidenberg ◽  
Alan Medlar ◽  
Ari Löytynoja
Keyword(s):  
Sequence Analysis ◽  
Data Visualization ◽  
Evolutionary Sequence ◽  
Integrated Platform

scholarly journals LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis

2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Eudes Barbosa ◽  
Richard Röttger ◽  
Anne-Christin Hauschild ◽  
Siomar de Castro Soares ◽  
Sebastian Böcker ◽  
...  
Keyword(s):  
Feature Selection ◽  
Sequence Analysis ◽  
Random Forest ◽  
Statistical Learning ◽  
Genomic Island ◽  
Robustness Analysis ◽  
Evolutionary Sequence ◽  
Free Living ◽  
Genomic Features ◽  
Model Tuning

AbstractDistinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features that might influence bacterial adaptation to a specific niche, we introduce LifeStyle-Specific-Islands (LiSSI). LiSSI combines evolutionary sequence analysis with statistical learning (Random Forest with feature selection, model tuning and robustness analysis). In summary, our strategy aims to identify conserved consecutive homology sequences (islands) in genomes and to identify the most discriminant islands for each lifestyle.

Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region

1999 ◽  
Vol 37 (2) ◽  
pp. 105-114 ◽  
Author(s):  
Y. GRAser ◽  
M. EL Fari ◽  
R. Vilgalys ◽  
A. F. A. Kuijpers ◽  
G. S. DE Hoog ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Its Region ◽  
The Family

Social Sequence Analysis

2015 ◽  
Author(s):  
Benjamin Cornwell
Keyword(s):  
Sequence Analysis

Ego Psychoanalytic Rorschach Interpretation

2017 ◽  
Vol 38 (1) ◽  
pp. 22-32 ◽  
Author(s):  
Irving B. Weiner
Keyword(s):  
Differential Diagnosis ◽  
Sequence Analysis ◽  
Treatment Planning ◽  
Well Being ◽  
Adjustment Difficulties ◽  
Behavioral Features ◽  
Defensive Style ◽  
Cognitive Slippage ◽  
Interpretive Process

Abstract. This article concerns the utility of ego psychoanalytic perspectives in Rorschach interpretation. Psychoanalytic ego psychology focuses on how people cope with events in their lives and how effectively they can meet challenges to their sense of well-being. The way people deal with experienced distress constitutes their defensive style and determines to a large extent what kind of person they are. Adequate defenses against anxiety promote comfortable and productive adjustment, whereas ineffective defenses typically cause adjustment difficulties and susceptibility to psychological disorders. In Rorschach assessment, the nature and effectiveness of a person’s defensive style can often be identified with a sequence analysis that integrates the structural, thematic, and behavioral features in the protocol. In particular, the sequential quality of responses, especially preceding and following instances of cognitive slippage, can help identify causes of upsetting concerns, defensive efforts to alleviating these concerns, and the adequacy of these defensive efforts in restoring equanimity. This interpretive process is illustrated with attention to implications for differential diagnosis and treatment planning in the Rorschach protocol of a 20-year-old suicidal woman.

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