RNA Secondary Structure Database, Analysis Tool-Set, and Case-Study Results on SARS-CoV-2

Author(s):  
Abdullah N. Arslan ◽  
Mutlu Mete ◽  
Anjali Kumari
Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Katherine E Richardson ◽  
Charles C Kirkpatrick ◽  
Brent M Znosko

Abstract The RNA Characterization of Secondary Structure Motifs, RNA CoSSMos, database is a freely accessible online database that allows users to identify secondary structure motifs among RNA 3D structures and explore their structural features. RNA CoSSMos 2.0 now requires two closing base pairs for all RNA loop motifs to create a less redundant database of secondary structures. Furthermore, RNA CoSSMos 2.0 represents an upgraded database with new features that summarize search findings and aid in the search for 3D structural patterns among RNA secondary structure motifs. Previously, users were limited to viewing search results individually, with no built-in tools to compare search results. RNA CoSSMos 2.0 provides two new features, allowing users to summarize, analyze and compare their search result findings. A function has been added to the website that calculates the average and representative structures of the search results. Additionally, users can now view a summary page of their search results that reports percentages of each structural feature found, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions. Other upgrades include a newly embedded NGL structural viewer, the option to download the clipped structure coordinates in *.pdb format and improved NMR structure results. RNA CoSSMos 2.0 is no longer simply a search engine for a structure database; it now has the capability of analyzing, comparing and summarizing search results. Database URL: http://rnacossmos.com


Author(s):  
NORMAN WILDE ◽  
SUZANNE W. DIETRICH ◽  
FRANK W. CALLISS

Since software engineers spend a large proportion of their time trying to understand computer programs, many tools have been proposed to help them with this task. The construction of such tools raises a series of specification and design issues and requires a careful choice among alternative user interfaces, tool architectures, and knowledge representations. This paper discusses the information needs of software engineers and describes and compares two such tools, the Extensible Dependency Analysis Tool Set (EDATS) and the Inter-Module Code Analysis system (IMCA). A case study is presented showing how each tool would be used to support typical program comprehension tasks. Though the two tools have quite similar objectives, their designs are radically different, leading to interesting contrasts in flexibility and ease of use.


Sensors ◽  
2021 ◽  
Vol 21 (23) ◽  
pp. 8006
Author(s):  
Evangelos Angelakis ◽  
Natalia Kotsani ◽  
Anastasia Georgaki

Singing voice is a human quality that requires the precise coordination of numerous kinetic functions and results in a perceptually variable auditory outcome. The use of multi-sensor systems can facilitate the study of correlations between the vocal mechanism kinetic functions and the voice output. This is directly relevant to vocal education, rehabilitation, and prevention of vocal health issues in educators; professionals; and students of singing, music, and acting. In this work, we present the initial design of a modular multi-sensor system for singing voice analysis, and describe its first assessment experiment on the ‘vocal breathiness’ qualitative characteristic. A system case study with two professional singers was conducted, utilizing signals from four sensors. Participants sung a protocol of vocal trials in various degrees of intended vocal breathiness. Their (i) vocal output, (ii) phonatory function, and (iii) respiratory behavior-per-condition were recorded through a condenser microphone (CM), an Electroglottograph (EGG), and thoracic and abdominal respiratory effort transducers (RET), respectively. Participants’ individual respiratory management strategies were studied through qualitative analysis of RET data. Microphone audio samples breathiness degree was rated perceptually, and correlation analysis was performed between sample ratings and parameters extracted from CM and EGG data. Smoothed Cepstral Peak Prominence (CPPS) and vocal folds’ Open Quotient (OQ), as computed with the Howard method (HOQ), demonstrated the higher correlation coefficients, when analyzed individually. DECOM method-computed OQ (DOQ) was also examined. Interestingly, the correlation coefficient of pitch difference between estimates from CM and EGG signals appeared to be (based on the Pearson correlation coefficient) statistically insignificant (a result that warrants investigation in larger populations). The study of multi-variate models revealed even higher correlation coefficients. Models studied were the Acoustic Breathiness Index (ABI) and the proposed multiple regression model CDH (CPPS, DOQ, and HOQ), which was attempted in order to combine analysis results from microphone and EGG signals. The model combination of ABI and the proposed CDH appeared to yield the highest correlation with perceptual breathiness ratings. Study results suggest potential for the use of a completed system version in vocal pedagogy and research, as the case study indicated system practicality, a number of pertinent correlations, and introduced topics with further research possibilities.


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