Search of Possible Insertions in Bacterial Genes

Eugene Korotkov; Yulia Suvorova; Maria Korotkova

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Paper

Search of Possible Insertions in Bacterial Genes

Topics: Sequence Analysis

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 0BIOSTEC, 99-108, 2014 , ESEO, Angers, Loire Valley, France

Authors: Eugene Korotkov ¹ ; Yulia Suvorova ² and Maria Korotkova ³

Affiliations: ¹ Centre of Bioengineering Russian Academy of Sciences and National Nuclear Investigational University (MIFI), Russian Federation ; ² Centre of Bioengineering Russian Academy of Sciences, Russian Federation ; ³ National Nuclear Investigational University (MIFI), Russian Federation

Keyword(s): Triplet Periodicity, Change Points, Sequence Analysis, Genes.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Sequence Analysis

Abstract: It is known that nucleotide sequences are not homogeneous and from this heterogeneity arises the task of segmentation of a sequence into a set of homogeneous parts by the points called change points. In the work we investigated a special case of change points in genes – paired change points (PCP). We used a well-known property of coding sequences – triplet periodicity. The sequence that we are especially interested in consists of three successive parts: the first and the last parts have similar triplet periodicity (TP) and the middle part is of another TP type. We aimed to find genes with PCP and provide explanation for the phenomenon. We developed a mathematical method for PCP detection based on new measure of similarity between TP matrixes. Among 66936 studied genes we found 2700 genes with PCP and 6459 genes with single change point (SCP). We suppose that PCP could be associated with double fusion or insertion events.

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Paper citation in several formats:

Korotkov, E.; Suvorova, Y. and Korotkova, M. (2014). Search of Possible Insertions in Bacterial Genes. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014) - BIOINFORMATICS; ISBN 978-989-758-012-3; ISSN 2184-4305, SciTePress, pages 99-108. DOI: 10.5220/0004721800990108

@conference{bioinformatics14,
author={Eugene Korotkov. and Yulia Suvorova. and Maria Korotkova.},
title={Search of Possible Insertions in Bacterial Genes},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014) - BIOINFORMATICS},
year={2014},
pages={99-108},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004721800990108},
isbn={978-989-758-012-3},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014) - BIOINFORMATICS
TI - Search of Possible Insertions in Bacterial Genes
SN - 978-989-758-012-3
IS - 2184-4305
AU - Korotkov, E.
AU - Suvorova, Y.
AU - Korotkova, M.
PY - 2014
SP - 99
EP - 108
DO - 10.5220/0004721800990108
PB - SciTePress