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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2012
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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/ |
format | Online Article Text |
id | pubmed-3532015 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
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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