GenFoSS - java application for presentation of coding stretches of never born proteins

• Autorzy: Piwowar M. , Matczyńska E. , Ochlawski P. , Kosibowicz M. , Kość D. , Swatowski M. , Więcek P. , Szepieniec T.
• Języki publikacji: EN

Abstrakty

EN

Application of genomes analysis results with respect to project of "never born protein" (NBP) is presented in this paper. GenFoSS application concerns visualisation of genomic sequence stretches that could encode proteins that are not observed in the Nature. The sequences of these proteins were generated randomly aimed to recognize the proteins of potential pharmacological activity. Identification of sequences similar to these of NBP can be viewed by GenFoSS application. GenFoSS gives information about sequence frequencies, percent identity, percent of similarity of alignments and E-value for aligned sequences. Comparison between two chromosomes in common organism and between different genomes as well can be done by these applications. There are also possibilities to check codon frequencies of nucleotide sequences that were found as a stretch of NBP.

Słowa kluczowe

EN

never born proteins; genomes analysis; nucleotide sequences distribution

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2008
• Tom: Vol. 4, no. 7
• Strony: 9--17
• Opis fizyczny: Bibliogr. 9 poz., rys.

Twórcy

autor

Piwowar M.

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

autor

Matczyńska E.

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

autor

Ochlawski P.

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

autor

Kosibowicz M.

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

autor

Kość D.

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

autor

Swatowski M.

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

autor

Więcek P.

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

autor

Szepieniec T.

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

Bibliografia

• [1] Piwowar M., Szepieniec T., Roterman-Konieczna I.: Massive identification of similarities in DNA materials organized in Grid environment. BAMS, 5, (2007).
• [2] Malawski M., Szepieniec T., Kochanczyk M., Piwowar M., Roterman-Konieczna I.: An approach to protein folding on the grid EUChinaGrid experience. BAMS, 5, (2007).
• [3] Roterman-Konieczna I., Kochanczyk M., Malawski M., Piwowar M., Szepieniec T: The Quest for Pharmacology Active 'Never Born Proteins' within EUChinaGRID Project, Grid Workshop; Krakow; October 15-18 2006.
• [4] 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, 519-528, (2006).
• [5] Altschul S.F., Gish W., Miller W., Myers E.W. & Lipman D.J.: Basic local alignment search tool. J. Mol. Biol. 215: 403-410, (1990).
• [6] The Genetic Codes: http://www.ncbi.nlm.nih.gov/Taxono-my/Utils/wprintgc.cgi?mode=c
• [7] Chiarabelli C, Vrijbloed J.W., De Lucrezia D., Thomas R.M., Stano P., Polticelli F., Ottone T., Papa E., Luisi P.L.: Investigation of de novo Totally Random Biosequences. Part II. On the Folding Frequency in a Totally Random Library of de novo Proteins Obtained by Phage Display. Chemistry & Biodiversity, 3, 840-859, (2006).
• [8] National Center of Biotechnology Information (ftp.ncbi.nih.gov).
• [9] 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).