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BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.

Oliveira JS, Araújo W, Lopes Sales AI, Brito Guerra Ad, Silva Araújo SC, de Vasconcelos AT, Agnez-Lima LF, Freitas AT - Database (Oxford) (2015)

Bottom Line: These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis.This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference.The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.

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Affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.

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Abundance analysis of an oil-contaminated soil sample. An important number of proteins involved in the synthesis of biosurfactants and alkane degradation have been identified.
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bav033-F1: Abundance analysis of an oil-contaminated soil sample. An important number of proteins involved in the synthesis of biosurfactants and alkane degradation have been identified.

Mentions: Figure 1 presents the Abundance Analysis of a metagenome dataset including a microbial consortium isolated from oil-contaminated soil. With this analysis it was possible to explicitly identify several biosurfactant synthesis pathways, enabling the identification of an important number of proteins involved in the synthesis of biosurfactants and alkane degradation.Figure 1.


BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.

Oliveira JS, Araújo W, Lopes Sales AI, Brito Guerra Ad, Silva Araújo SC, de Vasconcelos AT, Agnez-Lima LF, Freitas AT - Database (Oxford) (2015)

Abundance analysis of an oil-contaminated soil sample. An important number of proteins involved in the synthesis of biosurfactants and alkane degradation have been identified.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4381105&req=5

bav033-F1: Abundance analysis of an oil-contaminated soil sample. An important number of proteins involved in the synthesis of biosurfactants and alkane degradation have been identified.
Mentions: Figure 1 presents the Abundance Analysis of a metagenome dataset including a microbial consortium isolated from oil-contaminated soil. With this analysis it was possible to explicitly identify several biosurfactant synthesis pathways, enabling the identification of an important number of proteins involved in the synthesis of biosurfactants and alkane degradation.Figure 1.

Bottom Line: These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis.This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference.The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.

View Article: PubMed Central - PubMed

Affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.

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