VoGE - Java application for presentation of never born proteins gene structure elements

• Autorzy: Piwowar M. , Matczyńska E. , Pomański F. , Kośmider A. , Kość D. , Swatowski M. , Więcek P. , Szepieniec T.
• Języki publikacji: EN

Abstrakty

EN

VoGE application for visualizing gene structure elements in nucleotide sequences is presented in the paper. Genomic analyzing of genome sequences was continuation of proteomic efforts in the EuChinaGrid project that was oriented on the structure prediction of never born proteins, but probably with pharmacological application (there were 10**4 protein sequences generated which were used to create structures of that sequences). Finding of gene traces of never born proteins in all accessible sequenced genomes was one of the aim. As a results of searching genome materials there were found regions including protein-coding gene fragments that VoGE (Visualiser of Gene Elements) application presents. Graphical presentation of particular sequences enable user to see localization of coding NBP sequence and gene element composition in wider sequence context. Application interface and menu is intuitive so it seems to be easy to use.

Słowa kluczowe

EN

never born proteins; gene structure elements; gene finding

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2009
• Tom: Vol. 5, no. 10
• Strony: 9--13
• Opis fizyczny: Bibliogr. 6 poz., rys.

Twórcy

autor

Piwowar M.

• Department of Bioinformatics and Telemedicine, Jagiellonian University, Collegium Medicum,Sw. Anny 12, 31-008 Kraków, Poland

autor

Matczyńska E.

• Department of Bioinformatics and Telemedicine, Jagiellonian University, Collegium Medicum,Sw. Anny 12, 31-008 Kraków, Poland

autor

Pomański F.

• Faculty of Physics, Astronomy and Applied Informatics, Jagiellonian University, Reymonta 4, Kraków, Poland

autor

Kośmider A.

• Faculty of Physics, Astronomy and Applied Informatics, Jagiellonian University, Reymonta 4, Kraków, Poland

autor

Kość D.

• Faculty of Physics, Astronomy and Applied Informatics, Jagiellonian University, Reymonta 4, Kraków, Poland

autor

Swatowski M.

• Faculty of Physics, Astronomy and Applied Informatics, Jagiellonian University, Reymonta 4, Kraków, Poland

autor

Więcek P.

• Faculty of Physics, Astronomy and Applied Informatics, Jagiellonian University, Reymonta 4, Kraków, Poland

autor

Szepieniec T.

• Academic Computer Center CYFRONET, Nawojki 11, 30-950 Krakow, Poland

Bibliografia

• 1. Brylinski M., Jurkowski W., Konieczny L., Roterman I.: Limited conformational space for early-stage protein folding simulation, Bioinformatics, 20,199-205, 2004.
• 2. Brylinski M., Konieczny L, Roterman I.: Fuzzy-oil-drop hydrophobic force field - a model to represent late-stage folding (in silico) of lysozyme, J Biomol Struct Dyn, 23(5), 519-528, 2006.
• 3. Chiarabelli C, Vrijbloed J. W., Thomas R. M., Luisi P. L: Investigation of de novo totally random biosequences. Part I: A general method for in vitro selection of folded domains from a random polypeptide library displayed on phage, Chem Biodivers, 3, 827-839, 2006.
• 4. Chiarabelli C, Vrijbloed J. W., De Lucrezia D., Thomas R. M., Stano P., Polticelli R, Ottone I, Papa E., Luisi P. L: Investigation of de novo totally random biosequences. Part II: On the folding frequency in a totally random library of denovo proteins obtained by phage display, Chem Biodivers, 3, 840-859, 2006.
• 5. Burge C. and Karlin S.: Prediction of complete gene structures in human genomic DNA, J Mol Biol, 268, 78-94, 1997.
• 6. Altschul S. R, Gish W., Miller W., Myers E. W., Lipman D. J.: Basic local alignment search tool, J Mol Biol, Oct 5; 215(3): 403-10,1990.