A Scientometric Overview of Bioinformatics Tools in the Pseudomonas Putida Genome Study
Pseudomonas putida is a microorganism widely used in environmental science due to its high degradation power of recalcitrant compounds. This study aimed to perform a scientometric analysis of the global panorama of publications on the P. putida genome, in
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bstract. Pseudomonas putida is a microorganism widely used in environmental science due to its high degradation power of recalcitrant compounds. This study aimed to perform a scientometric analysis of the global panorama of publications on the P. putida genome, in addition to the bioinformatics tools mainly used. The growth of publications on the P. putida genome is continuous until 2020, being France, Spain and USA the main countries with publications on the subject. Illumina was the main sequencing platform used and, in this set of articles, 120 genomes were sequenced, 106 complete and 14 drafts. The main assembly software was SPAdes, comprising 23.3% of the articles, and NCBI PGAP was the main genome annotation tool, in 25% of the documents. Thus, this study allowed the visualization of the main bioinformatics tools used for the analysis of the P. putida genome, besides presenting the advance of the research on this subject, and also supporting next studies with P. putida. Keywords: Bioinformatic tools · Scientometric analysis · Pseudomonas putida
1 Introduction The planet is fighting against all types of environmental pollution, with the soil being one of the places most affected by environmental degradation. There is, therefore, a need to control soil pollution in order to maintain fertility as well as productivity [1, 2]. In this context, the development of technologies to remedy these degraded environments becomes indispensable [3]. Pseudomonas genera, belonging to the Gammaproteobacteria class, have been extensively studied over time due to their great potential for degradation and biotransformation of xenobiotic and recalcitrant compounds, and are likely to be used in various biotechnological processes of environmental recovery [4]. Pseudomonas putida is an ubiquitous bacterium, mainly in soil, classified as chemoorganotrophic, capable of metabolizing large carbon chains, as well as several recalcitrant pollutants [5]. From the sequencing of the genome, as well as from bioinformatics analyses, it is possible to know the proteins and metabolic pathways of Pseudomonas putida applied to environmental remediation and degradation of xenobiotic compounds [6]. Thus, © Springer Nature Switzerland AG 2020 J. C. Setubal and W. M. Silva (Eds.): BSB 2020, LNBI 12558, pp. 162–167, 2020. https://doi.org/10.1007/978-3-030-65775-8_15
A Scientometric Overview of Bioinformatics Tools
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using molecular level analysis it is possible to study new techniques and environmental applications for this organism [7]. This work aimed to perform a systematic analysis, by means of the scientometric methodology, of the global publications on the genome of Pseudomonas putida, analyzing mainly the bioinformatics tools used for the assembly and annotation of the sequenced genomes.
2 Methods The searches for performing the scientometric analysis were performed in the Web of Science database using the terms “Genome” AND “Pseudomonas putida” AND “soil”. Initially 159 documents were found on the researched terms, however, a manually filte
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