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

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated...

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Detalles Bibliográficos
Autores principales: Bhasi, Ashwini, Philip, Philge, Manikandan, Vinu, Senapathy, Periannan
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686582/
https://www.ncbi.nlm.nih.gov/pubmed/18984624
http://dx.doi.org/10.1093/nar/gkn746
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author Bhasi, Ashwini
Philip, Philge
Manikandan, Vinu
Senapathy, Periannan
author_facet Bhasi, Ashwini
Philip, Philge
Manikandan, Vinu
Senapathy, Periannan
author_sort Bhasi, Ashwini
collection PubMed
description We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/.
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spelling pubmed-26865822009-05-26 ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes Bhasi, Ashwini Philip, Philge Manikandan, Vinu Senapathy, Periannan Nucleic Acids Res Articles We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. Oxford University Press 2009-01 2008-11-04 /pmc/articles/PMC2686582/ /pubmed/18984624 http://dx.doi.org/10.1093/nar/gkn746 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Bhasi, Ashwini
Philip, Philge
Manikandan, Vinu
Senapathy, Periannan
ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
title ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
title_full ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
title_fullStr ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
title_full_unstemmed ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
title_short ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
title_sort exdom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686582/
https://www.ncbi.nlm.nih.gov/pubmed/18984624
http://dx.doi.org/10.1093/nar/gkn746
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