ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

Bhasi, Ashwini; Philip, Philge; Senapathy, Periannan

doi:10.1093/nar/gkn746

Cited by 12 publications

(9 citation statements)

References 32 publications

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“…Although there has been a rapid growth in the number of plant genome databases, such as PlantGDB (7), PLAZA (8), Phytozome (9) and GreenPhylDB (27), these resources lack comparative analytical capabilities for integrating protein domains from multiple species to investigate exon–intron structural evolution. ExDom (28) contains an extensive collection of exon–intron gene structures mapped to protein domains, but it primarily focuses on non-plant species. Furthermore, most related databases do not display the phylogenetic tree of gene families and orthologous gene evolution histories.…”

Section: Discussionmentioning

confidence: 99%

PIECE: a database for plant gene structure comparison and evolution

Wang¹,

You²,

Lazo³

et al. 2012

Nucleic Acids Research

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Gene families often show degrees of differences in terms of exon–intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes.

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Section: Discussionmentioning

confidence: 99%

PIECE: a database for plant gene structure comparison and evolution

Wang¹,

You²,

Lazo³

et al. 2012

Nucleic Acids Research

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“…Since inter-database comparative analysis would be very useful in plant genome analysis and knowledge discovery, we will implement link integration of RoBuST data to Gramene and Ensembl. We will also provide gateways to ExDom [ 31 ] a database resource that will enable the comparative functional analysis of proteins and domains from these genomes. Furthermore, we will enable the capability for analyzing mutations in genes, RNAs and regulatory sequences in RoBuST using the EuSplice resource [ 12 ] and comparative analysis of alternative splicing events using the AspAlt resource [ 32 ].…”

Section: Utility and Discussionmentioning

confidence: 99%

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

Bhasi¹,

Senalik

Simon

et al. 2010

BMC Plant Biol

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BackgroundRoot and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)—food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community.DescriptionThe RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers. The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3663 genes 5959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant species for comparative analysis of plant splicing patterns.ConclusionsRoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables.

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“…Several database tools have thus attempted to address the problem of studying the effect of alternative splicing on protein domains, e.g., ExDom 17 , ProSAS 18 , and ASPicDB 19 . However, ExDom 17 and ProSaS 18 were built around a decade ago on much smaller source databases, and at present they are down and no longer maintained.…”

Section: Introductionmentioning

confidence: 99%

DoChaP: The Domain Change Presenter

Gal-Oz

Haiat

Eliyahu

et al. 2020

Preprint

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Alternative RNA splicing results in multiple transcripts of the same gene, possibly encoding for different protein isoforms with different protein domains and functionalities. Whereas it is possible to manually determine the effect of a specific alternative splicing event on the domain composition of a particular encoded protein, the process requires the tedious integration of several data sources; it is therefore error prone and its implementation is 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), a web server for the visualization of the exon–domain association. DoChaP visualizes all transcripts of a given gene, the domains of the proteins that they encode, and the exons encoding each domain. The visualization enables a comparison between the transcripts and between the protein isoforms they encode for. The organization and visual presentation of the information makes the structural effect of each alternative splicing event on the protein structure easily identified. To enable a study of the conservation of the exon structure, alternative splicing, and the effect of alternative splicing on protein domains, DoChaP also facilitates an inter-species comparison of domain–exon associations. DoChaP thus provides a unique and easy-to-use visualization of the exon–domain association and its conservation between transcripts and orthologous genes and will facilitate the study of the functional effects of alternative splicing in health and disease.

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ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

Cited by 12 publications

References 32 publications

PIECE: a database for plant gene structure comparison and evolution

PIECE: a database for plant gene structure comparison and evolution

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

DoChaP: The Domain Change Presenter

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