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Genetic traces of never born proteins

Piwowar M., Matczyńska E., Malawski M., Szapieniec T., Roterman-Konieczna I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 2

79--87

EN

The presented results cover issues related to proteins that were “never born in nature”. The paper is focused on identifying genetic information stretches of protein sequences that were not identified to be existing in nature. The aim of the work was finding traces of “never born proteins” (NBP) everywhere in completely sequenced genomes including regions not expected as carrying the genetic information. The results of analyses relate to the search of the genetic material of species from different levels of the evolutionary tree from yeast through plant organisms up to the human genome. The analysis concerns searching the genome sequences. There are presented statistical details such as sequence frequencies, their length, percent identity and similarity of alignments, as well as E value of sequences found. Computations were performed on gLite-based grid environment. The results of the analyses showed that the NBP genetic record in the genomes of the studied organisms is absent at a significant level in terms of identity of contents and length of the sequences found. Most of the found sequences considered to be similar do not exceed 50% of the length of the NBP output sequences, which confirms that the genetic record of proteins is not accidental in terms of composition of gene sequences but also as regards the place of recording in genomes of living organisms.

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Ab initio protein structure prediction – the hydrophobicity distribution analysis

Evangelista G., Minervini G., Polticelli F, Malawski M., Szepieniec T., Flis Ł., Prymula K., Kochańczyk M., Matczyńska E., Wiśniowski Z., Salapa K., Banach M., Roterman I.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 2

5--12

EN

The three-dimensional structures generated for 20 “never born proteins” (NBP – random amino acid sequence with no significant homology to existing proteins) using two different techniques: ROSETTA (called R in the paper) and “fuzzy oil drop” model (called S in the paper) were compared to estimate the accordance with the assumed model estimating the influence of an external force field on the final structure of the protein. Selected structures are those corresponding to the highest (10 proteins) and lowest (10 proteins) RMS-D values obtained measuring the similarity between the R and S structures. The R structures generated according to an internal force field (the individual inter-molecular interaction) including solvation effects were analyzed using the “fuzzy oil drop” model as target model. The second applied model “fuzzy oil drop” generated structures characterized by an ordered hydrophobic core structure. 13 of the 20 selected S structures appeared to be accordant with the “fuzzy oil drop” model while 6 out of the 20 structures appeared to be accordant with external force field for R structures which suggests a general interpretation of the influence of an external force field on the folding simulation.

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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

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2009

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Vol. 5, no. 10

9--13

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.

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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

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2008

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Vol. 4, no. 7

9--17

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.