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Authors: Mikhail A. Golyshev 1 and Eugene V. Korotkov 2

Affiliations: 1 Russian Academy of Sciences, Russian Federation ; 2 Russian Academy of Sciences and National Research Nuclear University “MEPhI”, Russian Federation

Keyword(s): Genes, Annotation, DNA Similarity, Bacterial Genpmes, Phylagenetic Profile.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Sequence Analysis ; Systems Biology

Abstract: Over the last years a great number of bacterial genomes were sequenced. Now one of the most important challenges of computational genomics is the functional annotation of nucleic acid sequences. In this study we presented the computational method and the annotation system for predicting biological functions using phylogenetic profiles. The phylogenetic profile of a gene was created by way of searching for similarities between the nucleotide sequence of the gene and 1204 reference genomes, with further estimation of the statistical significance of found similarities. The profiles of the genes with known functions were used for prediction of possible functions and functional groups for the new genes.We conducted the functional annotation for genes from 104 bacterial genomes and compared the functions predicted by our system with the already known functions. For the genes that have already been annotated, the known function matched the function we predicted in 63% of the time, and in 86 % of the time the known function was found within the top five predicted functions. Besides, our system increased the share of annotated genes by 19%. The developed system may be used as an alternative or complementary system to the current annotation systems. (More)

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Paper citation in several formats:
A. Golyshev, M. and V. Korotkov, E. (2015). Computer Annotation of Nucleic Acid Sequences in Bacterial Genomes Using Phylogenetic Profiles. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2015) - BIOINFORMATICS; ISBN 978-989-758-070-3; ISSN 2184-4305, SciTePress, pages 134-143. DOI: 10.5220/0005236201340143

@conference{bioinformatics15,
author={Mikhail {A. Golyshev}. and Eugene {V. Korotkov}.},
title={Computer Annotation of Nucleic Acid Sequences in Bacterial Genomes Using Phylogenetic Profiles},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2015) - BIOINFORMATICS},
year={2015},
pages={134-143},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005236201340143},
isbn={978-989-758-070-3},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2015) - BIOINFORMATICS
TI - Computer Annotation of Nucleic Acid Sequences in Bacterial Genomes Using Phylogenetic Profiles
SN - 978-989-758-070-3
IS - 2184-4305
AU - A. Golyshev, M.
AU - V. Korotkov, E.
PY - 2015
SP - 134
EP - 143
DO - 10.5220/0005236201340143
PB - SciTePress

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