| URL: | http://redpet.bioinfo.pbf.hr/REDPET |
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| Description: | he database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. |
| Year founded: | 2018 |
| Last update: | |
| Version: | |
| Accessibility: |
Unaccessible
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| Country/Region: | Croatia |
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| University/Institution: | University of Zagreb |
| Address: | Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia |
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| Country/Region: | Croatia |
| Contact name (PI/Team): | Jurica Zucko |
| Contact email (PI/Helpdesk): | rh.fbp@okcuzj |
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Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from
Northern Adriatic Sea Sediments. [PMID: 30228802]
Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic -alkane degradation. The use of this system for bioprospecting was exemplified using potential and genes from this library. |