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MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for the Construction of Sequence Data Warehouses

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for the Construction of Sequence Data Warehouses


Titill: MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for the Construction of Sequence Data Warehouses
Höfundur: Gacesa, Ranko   orcid.org/0000-0003-2119-0539
Zucko, Jurica   orcid.org/0000-0001-7782-6503
Petursdottir, Solveig   orcid.org/0000-0003-4033-3654
Gudmundsdottir, Elisabet Eik   orcid.org/0000-0002-3404-850X
Fridjonsson, Olafur   orcid.org/0000-0002-8725-602X
Diminic, Janko   orcid.org/0000-0001-5104-5813
Long, Paul   orcid.org/0000-0001-6410-5803
Cullum, John   orcid.org/0000-0002-3850-8526
Hranueli, Daslav   orcid.org/0000-0001-8336-4384
Hreggvidsson, Gudmundur Oli   orcid.org/0000-0002-4958-1673
... 1 fleiri höfundar Sýna alla höfunda
Útgáfa: 2017-04
Tungumál: Enska
Umfang: 251-257
Háskóli/Stofnun: Háskóli Íslands
University of Iceland
Svið: Verkfræði- og náttúruvísindasvið (HÍ)
School of Engineering and Natural Sciences (UI)
Deild: Líf- og umhverfisvísindadeild (HÍ)
Faculty of Life and Environmental Sciences (UI)
Birtist í: Food Technology and Biotechnology;55(2)
ISSN: 1330-9862
1334-2606 (eISSN)
DOI: 10.17113/ftb.55.02.17.4749
Efnisorð: Bioprospecting; Carbohydrate-modifying enzymes; DNA assembly; DNA rannsóknir; Líftækni
URI: https://hdl.handle.net/20.500.11815/360

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Tilvitnun:

R. Gacesa et al.: MEGGASENSE, Food Technol. Biotechnol. 55 (2) 251–257 (2017). doi:10.17113/ftb.55.02.17.4749

Útdráttur:

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya. The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel ‘functional’ assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

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