VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features

Abstract Background Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protei...

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Bibliographic Details
Published in:	BMC genomics 2022-06, Vol.23 (1), p.1-472, Article 472
Main Authors:	Wang, Hongwei, Zhang, Xiaotian, Ding, Shuangcheng, Huang, Yujie, Wang, Shengyong, Chen, Huili, Chen, Yuhang, Li, Yuting
Format:	Article
Language:	eng
Subjects:	Amino acid sequence Analysis Annotations Applications programs Comparative genomic hybridization Datasets Evolutionary biology Format Genetic transcription Genomes Genomics Methods Molecular evolution Phylogenetics Protein domain Protein transport Proteins R (Programming language) R package Shiny application Software Transcript structure Visualization Visualization (Computers)
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Summary:	Abstract Background Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures. Results We developed a user-friendly, independent R package and Shiny web application named “VisProDom”. VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use. Conclusion VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics.
ISSN:	1471-2164 1471-2164