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ExonVisualiser – application for visualization exon units in 2D and 3D protein structures

The web application oriented on identification and visualization of protein regions encoded by exons is presented. The Exon Visualiser can be used for visualisation on different levels of protein structure: at the primary (sequence) level and secondary structures level, as well as at the level of te...

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Autores principales: Piwowar, Monika, Krzysztof, Porembski, Piotr, Piwowar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532015/
https://www.ncbi.nlm.nih.gov/pubmed/23275735
http://dx.doi.org/10.6026/97320630081280
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author Piwowar, Monika
Krzysztof, Porembski
Piotr, Piwowar
author_facet Piwowar, Monika
Krzysztof, Porembski
Piotr, Piwowar
author_sort Piwowar, Monika
collection PubMed
description The web application oriented on identification and visualization of protein regions encoded by exons is presented. The Exon Visualiser can be used for visualisation on different levels of protein structure: at the primary (sequence) level and secondary structures level, as well as at the level of tertiary protein structure. The programme is suitable for processing data for all genes which have protein expressions deposited in the PDB database. The procedure steps implemented in the application: I) loading exons sequences and theirs coordinates from GenBank file as well as protein sequences: CDS from GenBank and aminoacid sequence from PDB II) consensus sequence creation (comparing amino acid sequences form PDB file with the CDS sequence from GenBank file) III) matching exon coordinates IV) visualisation in 2D and 3D protein structures. Presented web-tool among others provides the color-coded graphical display of protein sequences and chains in three dimensional protein structures which are correlated with the corresponding exons. AVAILABILITY: http://149.156.12.53/ExonVisualiser/
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spelling pubmed-35320152012-12-28 ExonVisualiser – application for visualization exon units in 2D and 3D protein structures Piwowar, Monika Krzysztof, Porembski Piotr, Piwowar Bioinformation Software The web application oriented on identification and visualization of protein regions encoded by exons is presented. The Exon Visualiser can be used for visualisation on different levels of protein structure: at the primary (sequence) level and secondary structures level, as well as at the level of tertiary protein structure. The programme is suitable for processing data for all genes which have protein expressions deposited in the PDB database. The procedure steps implemented in the application: I) loading exons sequences and theirs coordinates from GenBank file as well as protein sequences: CDS from GenBank and aminoacid sequence from PDB II) consensus sequence creation (comparing amino acid sequences form PDB file with the CDS sequence from GenBank file) III) matching exon coordinates IV) visualisation in 2D and 3D protein structures. Presented web-tool among others provides the color-coded graphical display of protein sequences and chains in three dimensional protein structures which are correlated with the corresponding exons. AVAILABILITY: http://149.156.12.53/ExonVisualiser/ Biomedical Informatics 2012-12-19 /pmc/articles/PMC3532015/ /pubmed/23275735 http://dx.doi.org/10.6026/97320630081280 Text en © 2012 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Software
Piwowar, Monika
Krzysztof, Porembski
Piotr, Piwowar
ExonVisualiser – application for visualization exon units in 2D and 3D protein structures
title ExonVisualiser – application for visualization exon units in 2D and 3D protein structures
title_full ExonVisualiser – application for visualization exon units in 2D and 3D protein structures
title_fullStr ExonVisualiser – application for visualization exon units in 2D and 3D protein structures
title_full_unstemmed ExonVisualiser – application for visualization exon units in 2D and 3D protein structures
title_short ExonVisualiser – application for visualization exon units in 2D and 3D protein structures
title_sort exonvisualiser – application for visualization exon units in 2d and 3d protein structures
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532015/
https://www.ncbi.nlm.nih.gov/pubmed/23275735
http://dx.doi.org/10.6026/97320630081280
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