scholarly journals Phylogenetic and Protein Domain Architecture Analysis of Toll- like Receptor 4-10 Genes in Camel (Camelus dromedarius)

2021 ◽  
Vol 10 (01) ◽  
pp. 2887-2895
Author(s):  
Jyoti Choudhary ◽  
Mukul Purva ◽  
Mahendra Milind ◽  
Kritika Gahlot ◽  
Taruna Bhati ◽  
...  
Keyword(s):  
Domain Architecture ◽  
Protein Domain ◽  
Camelus Dromedarius ◽  
Toll Like Receptor ◽  
Toll Like Receptor 4 ◽  
Protein Domain Architecture ◽  
Architecture Analysis

scholarly journals TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses

2020 ◽  
Vol 48 (W1) ◽  
pp. W72-W76 ◽  
Author(s):  
Vadim M Gumerov ◽  
Igor B Zhulin
Keyword(s):  
Protein Function ◽  
Computational Study ◽  
Function Analysis ◽  
Domain Architecture ◽  
Protein Domain ◽  
Homologous Proteins ◽  
Gene Neighborhood ◽  
Protein Domain Architecture ◽  
Key Steps

Abstract Key steps in a computational study of protein function involve analysis of (i) relationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods the corresponding proteins are encoded in. Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary data and combine them by hand, which is time-consuming and error-prone. Here, we present a new platform, TREND (tree-based exploration of neighborhoods and domains), which can perform all the necessary steps in automated fashion and put the derived information into phylogenomic context, thus making evolutionary based protein function analysis more efficient. A rich set of adjustable components allows a user to run the computational steps specific to his task. TREND is freely available at http://trend.zhulinlab.org.

scholarly journals Evolutionary dynamics of protein domain architecture in plants

2012 ◽  
Vol 12 (1) ◽  
pp. 6 ◽  
Author(s):  
Xue-Cheng Zhang ◽  
Zheng Wang ◽  
Xinyan Zhang ◽  
Mi Ha Le ◽  
Jianguo Sun ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Domain Architecture ◽  
Protein Domain ◽  
Protein Domain Architecture

scholarly journals SMART: recent updates, new developments and status in 2020

2020 ◽  
Vol 49 (D1) ◽  
pp. D458-D460 ◽  
Author(s):  
Ivica Letunic ◽  
Supriya Khedkar ◽  
Peer Bork
Keyword(s):  
Domain Architecture ◽  
Protein Domains ◽  
Mobile Element ◽  
Protein Domain ◽  
Modular Architecture ◽  
Comprehensive Overview ◽  
Web Resource ◽  
New Models ◽  
Analysis Mode ◽  
Architecture Analysis

Abstract SMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curated models for more than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART’s vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.

scholarly journals DAVI: a tool for clustering and visualising protein domain architectures

2021 ◽  
Author(s):  
Nathan Jawadi Chadi ◽  
Paul Saighi ◽  
Fabio Rocha Jimenez Vieira ◽  
Juliana Silva Bernardes
Keyword(s):  
Domain Architecture ◽  
Protein Sequences ◽  
Protein Domain ◽  
Computational Approaches ◽  
Prediction Tools ◽  
Protein Functions ◽  
Visualization Tools ◽  
Protein Domain Architecture ◽  
User Friendly

The characterization of protein functions is one of the main challenges in bioinformatics. Proteins are often composed of individual units termed domains, motifs that can evolve independently. The domain architecture of a given protein is the particular order and the content of its numerous domains. Some computational approaches predict the most likely domain architecture for a set of proteins. However, a few numbers of visualization tools exist, and most of them are unavailable. Here we present DAVI, an efficient and user-friendly web server for protein domain architecture clustering and visualization. DAVI accepts the output of most used domain architecture prediction tools and also produces domain architectures for a set of protein sequences. It provides a rich visualization for comparing, analyzing, and visualizing domain architectures.

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