DoChaP: the domain change presenter

• Published in: Nucleic acids research 2021-07, Vol.49 (W1), p.W162-W168
• Main Authors: Gal-Oz, Shani T, Haiat, Nimrod, Eliyahu, Dana, Shani, Guy, Shay, Tal
• Format: Article
• Language: English
• Subjects: Web Server Issue
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkab357

Abstract Alternative splicing results in multiple transcripts of the same gene, possibly encoding for different protein isoforms with different domains. Whereas it is possible to manually determine the effect of alternative splicing on the domain composition for a single event, the process requires the tedious integration of several data sources; it is error prone and not feasible for genome-wide characterization of domains affected by differential splicing. To fulfill the need for an automated solution, we developed the Domain Change Presenter (DoChaP, https://dochap.bgu.ac.il/), a web server for the visualization of exon–domain associations. DoChaP visualizes all transcripts of a given gene, the encoded proteins and their domains, and enables a comparison between the transcripts and between their protein products. The colors and organization make the structural effect of alternative splicing events on protein structures easily identified. To enable the study of the conservation of exons structure, alternative splicing, and the effect of alternative splicing on protein domains, DoChaP also provides a two-species comparison of exon–domain associations. DoChaP thus provides a unique and easy-to-use visualization of the exon–domain association and conservation, and will facilitate the study of the structural effects of alternative splicing in health and disease. Graphical Abstract Graphical Abstract Overview. (A) The DoChaP-database (DoChaP-db) integrates information on transcripts and protein domains from several sources into a single SQLite database. (B) Genes, transcripts, exons, proteins and domain events data was taken from NCBI and Ensembl. Orthology information was taken from Ensembl Compara. Domain types and the mapping of the domain accessions from different sources (Pfam, SMART, CDD and TIGRFAMs) was inferred from InterPro. (C) A simple visualization of the information collected into the DoChaP-db is presented in the DoChaP webserver for a user selected gene. The visualization presents the genomic context of the transcripts (Gene) and the exon structure of the coding region of the mature mRNA of all the transcripts (T1, T2) and their encoded protein domain composition (P1, P2). Exons are represented in different colors, and their encoded protein domains are represented by the corresponding colors. (D) The 'species comparison' feature allows the user to select a gene and a species and visualize the orthologous genes so as to enable a comparison of t