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CleanBSequences: an efficient curator of biological sequences in R

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Abstract

This work presents a new method and tool to solve a common problem of molecular biologists and geneticists who use molecular markers in their scientific research and developments: curation of sequences. Omic studies conducted by molecular biologists and geneticists usually involve the use of molecular markers. AFLP, cDNA-AFLP, and MSAP are examples of markers that render information at the genomics, transcriptomics, and epigenomics levels, respectively. These three types of molecular markers use adaptors that are the template for PCR amplification. The sequences of the adaptors have to be eliminated for the analysis of the results. Since a large number of sequences are usually obtained in these studies, this clean-up of the data could demand long time and work. To automate this work, an R package, named CleanBSequences, was created that allows the sequences to be curated massively, quickly, without errors and can be used offline. The curating is performed by aligning the forward and/or reverse primers or ends of cloning vectors with the sequences to be removed. After the alignment, new subsequences are generated without biological fragments not desired by the user, i.e., sequences needed by the techniques. In conclusion, the CleanBSequences tool facilitates the work of researchers, reducing time, effort, and working errors. Therefore, the present tool would respond to the problems related to the curation of sequences obtained from the use of some types of molecular markers. In addition to the above, being an open source, CleanBSequences is a flexible tool that has the potential to be used in future improvements to respond to new problems.

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Acknowledgements

This work was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas grants number [PIP11220090100613] and [PUE22920160100043CO (IICAR)], and the Agencia Nacional de Promoción Científica y Tecnológica [PICT20121321].

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Authors and Affiliations

  1. Instituto de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km. 3, 2580, Marcos Juárez, Córdoba, Argentina

    Florencia I. Pozzi

  2. Cátedra de Microbiología, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina

    Florencia I. Pozzi

  3. Cátedra de Epidemiología, Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, S2170, Casilda, Santa Fe, Argentina

    Gisela Y. Green

  4. Cátedra de Estadística, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina

    Ivana G. Barbona

  5. Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) (CONICET-UNR), Zavalla, Argentina

    Gustavo R. Rodríguez & Silvina A. Felitti

  6. Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina

    Gustavo R. Rodríguez

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  1. Florencia I. Pozzi
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  2. Gisela Y. Green
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  3. Ivana G. Barbona
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  4. Gustavo R. Rodríguez
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  5. Silvina A. Felitti
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Correspondence to Florencia I. Pozzi.

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Pozzi, F.I., Green, G.Y., Barbona, I.G. et al. CleanBSequences: an efficient curator of biological sequences in R. Mol Genet Genomics 295, 837–841 (2020). https://doi.org/10.1007/s00438-020-01671-z

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  • DOI: https://doi.org/10.1007/s00438-020-01671-z

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