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International Work-Conference on Bioinformatics and Biomedical Engineering

IWBBIO 2019: Bioinformatics and Biomedical Engineering pp 370–378Cite as

Triplet Frequencies Implementation in Total Transcriptome Analysis

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11465))

Abstract

We studied the structuredness in total transcriptome of Siberian larch. To do that, the contigs from total transcriptome has been labeled with the reads comprising the tissue specific transcriptomes, and the distribution of the contigs from the total transcriptome has been developed with respect to the mutual entropy of the frequencies of occurrence of reads from tissue specific transcriptomes. It was found that a number of contigs contain comparable amounts of reads from different tissues, so the chimeric transcripts to be extremely abundant. On the contrary, the transcripts with high tissue specificity do not yield a reliable clustering revealing the tissue specificity. This fact makes usage of total transcriptome for the purposes of differential expression arguable.

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Author information

Authors and Affiliations

  1. Institute of Computational Modelling of SB RAS, Akademgorodok, 660036, Krasnoyarsk, Russia

    Michael Sadovsky

  2. Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodny prosp., 79, 660049, Krasnoyarsk, Russia

    Michael Sadovsky, Tatiana Guseva & Vladislav Biriukov

Authors
  1. Michael Sadovsky
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  2. Tatiana Guseva
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  3. Vladislav Biriukov
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Corresponding author

Correspondence to Michael Sadovsky .

Editor information

Editors and Affiliations

  1. Department of Computer Architecture and Computer Technology Higher Technical School of Information Technology and Telecommunications Engineering, CITIC-UGR, Granada, Spain

    Ignacio Rojas

  2. ETSIIT, University of Granada, Granada, Spain

    Olga Valenzuela

  3. CITIC-UGR, University of Granada, Granada, Spain

    Fernando Rojas

  4. Fundacion Progreso y Salud, Granada, Spain

    Francisco Ortuño

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Sadovsky, M., Guseva, T., Biriukov, V. (2019). Triplet Frequencies Implementation in Total Transcriptome Analysis. In: Rojas, I., Valenzuela, O., Rojas, F., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2019. Lecture Notes in Computer Science(), vol 11465. Springer, Cham. https://doi.org/10.1007/978-3-030-17938-0_33

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  • DOI: https://doi.org/10.1007/978-3-030-17938-0_33

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-17937-3

  • Online ISBN: 978-3-030-17938-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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