Bioinformatics applied to biotechnology: A review towards bioenergy research

Carvalho, Lucas Miguel de; Borelli, Guilherme; Camargo, Antônio Pedro; Assis, Michelle Alexandrino de; Ferraz, S.M.F. de; Fiamenghi, Mateus Bernabe; José, Juliana; Mofatto, Luciana Souto; Nagamatsu, Sheila Tiemi; Persinoti, Gabriela Félix; Silva, Nicholas Vinícius; Vasconcelos, Adrielle Ayumi de; Pereira, Gonçalo Amarante Guimarães; Carazzolle, Marcelo F.

doi:10.1016/j.biombioe.2019.02.016

Cited by 28 publications

(20 citation statements)

References 439 publications

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“…Unlike the genome, the transcriptome is highly dynamic and actively changes as a consequence of factors that influence the stage of development of organisms, as well as the surrounding environmental conditions. In this sense, transcriptomics is an essential tool to interpret the functional elements of the genome, having as object of study, all species of transcripts, messenger RNA, non-coding RNA and small RNAs [26]. Its main purpose being to determine transcriptional structure of genes, that is, where a gene begins and ends (start sites 5′ and 3′ end), posttranscriptional modifications, splicing patterns and differential expression analysis [27].…”

Section: Transcriptome Data Analysismentioning

confidence: 99%

Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins

Hernández-Domínguez¹,

Castillo-Ortega²,

García-Esquivel³

et al. 2020

Computational Biology and Chemistry

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This chapter deals with the topic of bioinformatics, computational, mathematics, and statistics tools applied to biology, essential for the analysis and characterization of biological molecules, in particular proteins, which play an important role in all cellular and evolutionary processes of the organisms. In recent decades, with the next generation sequencing technologies and bioinformatics, it has facilitated the collection and analysis of a large amount of genomic, transcriptomic, proteomic, and metabolomic data from different organisms that have allowed predictions on the regulation of expression, transcription, translation, structure, and mechanisms of action of proteins as well as homology, mutations, and evolutionary processes that generate structural and functional changes over time. Although the information in the databases is greater every day, all bioinformatics tools continue to be constantly modified to improve performance that leads to more accurate predictions regarding protein functionality, which is why bioinformatics research remains a great challenge.

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Section: Transcriptome Data Analysismentioning

confidence: 99%

Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins

Hernández-Domínguez¹,

Castillo-Ortega²,

García-Esquivel³

et al. 2020

Computational Biology and Chemistry

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“…Ao planejar um experimento de RNA-seq para análise de expressão diferencial é importante considerar a quantidade de réplicas que serão sequenciadas, considerando que, em geral, para que todos os genes encontrados sejam relevantes, pede-se um mínimo de 12 réplicas (Schurch, et al, 2016). (Carvalho, et al, 2019). Dessa forma, o pipeline apresentado pode ser adaptado de acordo com as necessidades do projeto, adequação aos dados e preferência do usuário, sendo de extrema relevância para estudos com plantas.…”

Section: Adaptação Do Pipeline Em Diferentes Contextosunclassified

Avaliação De Gradiente Pedoambiental Usando Análise De Componentes Principais (Pca) Na Antártica Marítima

Schmitz¹,

Wang²,

Schaefer³

et al. 2020

Aplicações Da Linguagem R Em Análises De Vegetação

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“…Much research has identified and characterized sets of proteins composing the proteome of a cell, an organelle or a tissue [29]. As mentioned previously, prior to MS analysis, proteins extracted from a biological sample may be separated and digested followed by peptide sequencing using MS/MS and automated database searching.…”

Section: Proteomic Profile Analysis Of Macroalgaementioning

confidence: 99%

“…Thus, advancements in DNA and RNA sequencing along with mass spectrometry (MS), supported by high-performance computing, allowed the identification of new metabolic processes in many organisms, expanding the knowledge of biological systems [29]. Large-scale biological data together with associated bioinformatics analysis are known by the “-omics” suffix and comprise genomics, metagenomics, phylogenomics, transcriptomics, proteomics, and metabolomics [29]. In the present review, the application of proteomic and transcriptomic fields in macroalgae research will be particularly discussed.…”

Section: Introductionmentioning

confidence: 99%

Insights into the Regulation of Algal Proteins and Bioactive Peptides Using Proteomic and Transcriptomic Approaches

Beaulieu

2019

Molecules

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Oceans abound in resources of various kinds for R&D and for commercial applications. Monitoring and bioprospecting allow the identification of an increasing number of key natural resources. Macroalgae are essential elements of marine ecosystems as well as a natural resource influenced by dynamic environmental factors. They are not only nutritionally attractive but have also demonstrated potential health benefits such as antioxidant, antihypertensive, and anti-inflammatory activities. Several bioactive peptides have been observed following enzymatic hydrolysis of macroalgal proteins. In addition, significant differences in protein bioactivities and peptide extracts of wild and cultivated macroalgae have been highlighted, but the metabolic pathways giving rise to these bioactive molecules remain largely elusive. Surprisingly, the biochemistry that underlies the environmental stress tolerance of macroalgae has not been well investigated and remains poorly understood. Proteomic and functional genomic approaches based on identifying precursor proteins and bioactive peptides of macroalgae through integrated multi-omics analysis can give insights into their regulation as influenced by abiotic factors. These strategies allow evaluating the proteomics profile of regulation of macroalgae in response to different growth conditions as well as establishing a comparative transcriptome profiling targeting structural protein-coding genes. Elucidation of biochemical pathways in macroalgae could provide an innovative means of enhancing the protein quality of edible macroalgae. This could be ultimately viewed as a powerful way to drive the development of a tailored production and extraction of high value molecules. This review provides an overview of algal proteins and bioactive peptide characterization using proteomics and transcriptomic analyses.

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Bioinformatics applied to biotechnology: A review towards bioenergy research

Cited by 28 publications

References 439 publications

Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins

Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins

Avaliação De Gradiente Pedoambiental Usando Análise De Componentes Principais (Pca) Na Antártica Marítima

Insights into the Regulation of Algal Proteins and Bioactive Peptides Using Proteomic and Transcriptomic Approaches

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