MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data

Abstract

The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information.

Selenoproteins of African trypanosomes are dispensable for parasite survival in a mammalian host

“…Blastp and psi-blast homology searches were performed using the full-length or sequence domains of Seltryp as a query against eukaryotic and prokaryotic genomes deposited at NCBI and in the integrated microbial genomes data base [16], respectively. The identified sequences were retroblasted against kinetoplastid genomes to obtain the best reciprocal hits.…”

Genome Identifier: A Tool for Phylogenetic Analysis of Microbial Genomes

“…We constructed 36 phylogenetic trees for 36 prokaryotic genomes. The prokaryotes were automatically chosen (Table 1) using "choose one genome for each phylum" in the MBGD taxonomy browser [27], and unclassified species were excluded. Genome sequence data of the 36 species in FASTA format were obtained from the NCBI database.…”

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

“…Escherichia coli and Bacillus subtilis m 5 U modification enzymes were used in blastp searches for mollicutes homologs in the MolliGen (http://molligen.org) database [45]. MolliGen and MBGD (http://mbgd.genome.ad.jp/) [46] databases were used to study the genomic contexts of genes of interest. The phylogenetic tree of mollicutes was generated using the maximum likelihood method from the concatenated multiple sequence alignments of 79 selected orthologous proteins involved in translation [47].…”