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MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.
Food Technology and Biotechnology ( IF 2.4 ) Pub Date : 2017-9-5 , DOI: 10.17113/ftb.55.02.17.4749
Ranko Gacesa 1, 2 , Jurica Zucko 1, 3 , Solveig K Petursdottir 4 , Elisabet Eik Gudmundsdottir 4 , Olafur H Fridjonsson 4 , Janko Diminic 1, 3 , Paul F Long 2, 5 , John Cullum 6 , Daslav Hranueli 1, 3 , Gudmundur O Hreggvidsson 4, 7 , Antonio Starcevic 1, 3
Affiliation  

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.

中文翻译:

MEGGASENSE-元基因组/基因组注释序列自然语言搜索引擎:用于构建序列数据仓库的平台。

MEGGASENSE平台可构建DNA或蛋白质序列的关系数据库。默认的功能分析基于KEGG数据库中的序列使用14106个隐藏的马尔可夫模型(HMM)配置文件。Solr搜索引擎允许进行复杂的查询,并且还集成了BLAST搜索功能。这些标准功能用于从牛链霉菌的预测蛋白质组生成SCATT数据库。描述了用于糖修饰酶的生物勘探的专门的元基因组数据库(AMYLOMICS)的实现。除了标准的阅读组装外,还开发了一种新颖的“功能”组装,其中在组装之前进行了带有HMM轮廓的阅读筛选。AMYLOMICS数据库结合了用于糖修饰酶的其他HMM谱图,并说明了HMM和BLAST分析的组合如何帮助鉴定有趣的基因。MEGGASENSE已经生成了各种不同的蛋白质组和元基因组数据库。
更新日期:2020-08-21
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