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Artículo

CleanBSequences: an efficient curator of biological sequences in R

Pozzi, Florencia IleanaIcon ; Green, Gisela YaelIcon ; Barbona, Ivana Gabriela; Rodríguez, Gustavo RubénIcon ; Felitti, Silvina AndreaIcon
Fecha de publicación: 04/2020
Editorial: Springer Heidelberg
Revista: Molecular Genetics And Genomics
ISSN: 1617-4615
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Ciencias de la Información y Bioinformática

Resumen

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.
Palabras clave: AFLP , BIOLOGICAL SEQUENCES , CDNA-AFLP , CURATION , MSAP , R
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info:eu-repo/semantics/restrictedAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/163305
URL: http://link.springer.com/10.1007/s00438-020-01671-z
DOI: http://dx.doi.org/10.1007/s00438-020-01671-z
Colecciones
Articulos(CCT - CORDOBA)
Articulos de CTRO.CIENTIFICO TECNOL.CONICET - CORDOBA
Articulos(IICAR)
Articulos de INST. DE INVESTIGACIONES EN CIENCIAS AGRARIAS DE ROSARIO
Citación
Pozzi, Florencia Ileana; Green, Gisela Yael; Barbona, Ivana Gabriela; Rodríguez, Gustavo Rubén; Felitti, Silvina Andrea; CleanBSequences: an efficient curator of biological sequences in R; Springer Heidelberg; Molecular Genetics And Genomics; 295; 4; 4-2020; 837-841
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