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Title

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

 

Authors

Monika Piwowar1*, Porembski Krzysztof1 & Piwowar Piotr2

 

Affiliation

1Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland; 2Department of Measurement and Electronics, AGH University of Science and Technology, al. A. Mickiewicza 30, 30-059 Krakow, Poland.

 

Email

mpiwowar@cm-uj.krakow.pl; *Corresponding author

 

Article Type

Software

Date

Received November 12, 2012; Accepted November 14, 2012; Published December 19, 2012

 

Abstract

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/

 

Keywords

Exon visualisation, Exon unit identification in proteins

 

Citation

Piwowar et al. Bioinformation 8(25): 1280-1282 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.