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Food Technology and Biotechnology, Vol. 55 No. 2, 2017.

Short communication, Note

https://doi.org/10.17113/ftb.55.02.17.4749

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

Ranko Gacesa ; SemGen Ltd., Lanište 5/D, HR-10 000 Zagreb, Croatia
Jurica Zucko orcid id orcid.org/0000-0001-7782-6503 ; SemGen Ltd., Lanište 5/D, HR-10 000 Zagreb, Croatia
Solveig K. Petursdottir ; Matis Ltd., Vínlandsleið 12, IS-113 Reykjavík, Iceland
Elisabet Eik Gudmundsdottir ; Matis Ltd., Vínlandsleið 12, IS-113 Reykjavík, Iceland
Olafur H. Fridjonsson ; Matis Ltd., Vínlandsleið 12, IS-113 Reykjavík, Iceland
Janko Diminic ; SemGen Ltd., Lanište 5/D, HR-10 000 Zagreb, Croatia
Paul F. Long ; Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
John Cullum ; Department of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, Germany
Daslav Hranueli ; SemGen Ltd., Lanište 5/D, HR-10 000 Zagreb, Croatia
Gudmundur O. Hreggvidsson ; Matis Ltd., Vínlandsleið 12, IS-113 Reykjavík, Iceland
Antonio Starcevic ; SemGen Ltd., Lanište 5/D, HR-10 000 Zagreb, Croatia

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Abstract

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.

Keywords

bioprospecting; carbohydrate-modifying enzymes; DNA assembly

Hrčak ID:

183073

URI

https://hrcak.srce.hr/183073

Publication date:

14.6.2017.

Article data in other languages: croatian

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