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

Piwowar M., Matczyńska E., Pomański F., Kośmider A., Kość D., Swatowski M., Więcek P., Szepieniec T.

Bio-Algorithms and Med-Systems

2009

Vol. 5, no. 10

9--13

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.

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

Piwowar M., Matczyńska E., Ochlawski P., Kosibowicz M., Kość D., Swatowski M., Więcek P., Szepieniec T.

Bio-Algorithms and Med-Systems

2008

Vol. 4, no. 7

9--17

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.