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Authors: Małgorzata Wańczyk ; Paweł Błażej ; Paweł Mackiewicz and Stanisław Cebrat

Affiliation: University of Wrocław, Poland

Keyword(s): Gene finding, Coding potential, Small ORFs, Short genes.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Pattern Recognition, Clustering and Classification ; Sequence Analysis

Abstract: Current ’classical’ algorithms recognizing protein coding sequences do not work effectively with sequences of small length. To deal with this problem we have proposed some improvements of the existing gene finders without any assumed arbitrary threshold. Introduced parameters describe position of tested sequences in the ranking of all small Open Reading Frames and short protein coding genes found in the analyzed genome. The sequences can be ranked according to the coding potential calculated by ’standard’ gene prediction algorithms. As an example, we used two algorithms for gene recognition and tested the set of selected small ORFs which were selected from prokaryotic genomes using sequence similarity methods. The applied approach enabled to identify promising sequence that can code for small proteins.

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Paper citation in several formats:
Wańczyk, M., Błażej, P., Mackiewicz, P. and Cebrat, S. (2012). HOW TO DEAL WITH SMALL OPEN READING FRAMES?. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS; ISBN 978-989-8425-90-4; ISSN 2184-4305, SciTePress, pages 246-250. DOI: 10.5220/0003856202460250

@conference{bioinformatics12,
author={Małgorzata Wańczyk and Paweł Błażej and Paweł Mackiewicz and Stanisław Cebrat},
title={HOW TO DEAL WITH SMALL OPEN READING FRAMES?},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS},
year={2012},
pages={246-250},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003856202460250},
isbn={978-989-8425-90-4},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS
TI - HOW TO DEAL WITH SMALL OPEN READING FRAMES?
SN - 978-989-8425-90-4
IS - 2184-4305
AU - Wańczyk, M.
AU - Błażej, P.
AU - Mackiewicz, P.
AU - Cebrat, S.
PY - 2012
SP - 246
EP - 250
DO - 10.5220/0003856202460250
PB - SciTePress

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