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

Uchiyama I, Mihara M, Nishide H, Chiba H - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan uchiyama@nibb.ac.jp.

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An example session of the MyMBGD analysis, where comparison of Staphylococcus aureus genomes was performed focusing on two strains, 930918-3 and D30, which are indicated with ‘a’ and ‘b’, respectively. (A) The MyMBGD interface for specifying a set of genomes in taxon-specific comparison mode. Complete genomes are shown in light yellow and draft genomes are shown in light blue. (B) Occurrence-pattern display in which ortholog groups that are present in strain D30 and absent in strain 930918-3 are extracted and summarized according to occurrence pattern. The occurrence pattern corresponding to the transposon-like cluster containing the FtsK/SpoIIIE family protein is indicated with ‘x’. (C) Genome region map comparison viewer showing gene order conservation around the ortholog group of the FtsK/SpoIIIE family protein. Here, orthologous genes are drawn in the same color and pattern.
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Figure 4: An example session of the MyMBGD analysis, where comparison of Staphylococcus aureus genomes was performed focusing on two strains, 930918-3 and D30, which are indicated with ‘a’ and ‘b’, respectively. (A) The MyMBGD interface for specifying a set of genomes in taxon-specific comparison mode. Complete genomes are shown in light yellow and draft genomes are shown in light blue. (B) Occurrence-pattern display in which ortholog groups that are present in strain D30 and absent in strain 930918-3 are extracted and summarized according to occurrence pattern. The occurrence pattern corresponding to the transposon-like cluster containing the FtsK/SpoIIIE family protein is indicated with ‘x’. (C) Genome region map comparison viewer showing gene order conservation around the ortholog group of the FtsK/SpoIIIE family protein. Here, orthologous genes are drawn in the same color and pattern.

Mentions: Figure 4 shows an example session of the taxon-specific comparison mode in the new MyMBGD interface, where strains of Staphylococcus aureus including five draft genomes and 48 complete genomes are specified for comparison (Figure 4A). Here, these draft genomes include strains D30 and 930918-3, which have been investigated as models for nasal carrier and noncarrier strains, respectively (20). S. aureus is a versatile human pathogen and its infection in hospitals and the emergence of drug-resistant strains poses a worldwide problem. Comparison of these two strains is interesting in terms of infectious mechanisms because the presence of S. aureus in the nose increases the risk of its infection (21). After ortholog clustering among these genomes is completed, occurrence (presence/absence) pattern analysis can be conducted on the cluster map page; in this example, ortholog groups included in the D30 strain but not in the 930918-3 strain are extracted and displayed (Figure 4B). For some ortholog groups in which a user is interested, a detailed analysis can be conducted using any functionality in MBGD. In this example, by selecting a particular occurrence pattern (indicated with ‘x’ in Figure 4B), one can identify a transposon-like cluster carrying several genes including a FtsK/SpoIIIE family protein and TraG protein, which was listed as an interesting observation by the original authors (20). The arrangement of these genes in each chromosome can then be compared on the genome region map comparison viewer (Figure 4C).


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

Uchiyama I, Mihara M, Nishide H, Chiba H - Nucleic Acids Res. (2014)

An example session of the MyMBGD analysis, where comparison of Staphylococcus aureus genomes was performed focusing on two strains, 930918-3 and D30, which are indicated with ‘a’ and ‘b’, respectively. (A) The MyMBGD interface for specifying a set of genomes in taxon-specific comparison mode. Complete genomes are shown in light yellow and draft genomes are shown in light blue. (B) Occurrence-pattern display in which ortholog groups that are present in strain D30 and absent in strain 930918-3 are extracted and summarized according to occurrence pattern. The occurrence pattern corresponding to the transposon-like cluster containing the FtsK/SpoIIIE family protein is indicated with ‘x’. (C) Genome region map comparison viewer showing gene order conservation around the ortholog group of the FtsK/SpoIIIE family protein. Here, orthologous genes are drawn in the same color and pattern.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383954&req=5

Figure 4: An example session of the MyMBGD analysis, where comparison of Staphylococcus aureus genomes was performed focusing on two strains, 930918-3 and D30, which are indicated with ‘a’ and ‘b’, respectively. (A) The MyMBGD interface for specifying a set of genomes in taxon-specific comparison mode. Complete genomes are shown in light yellow and draft genomes are shown in light blue. (B) Occurrence-pattern display in which ortholog groups that are present in strain D30 and absent in strain 930918-3 are extracted and summarized according to occurrence pattern. The occurrence pattern corresponding to the transposon-like cluster containing the FtsK/SpoIIIE family protein is indicated with ‘x’. (C) Genome region map comparison viewer showing gene order conservation around the ortholog group of the FtsK/SpoIIIE family protein. Here, orthologous genes are drawn in the same color and pattern.
Mentions: Figure 4 shows an example session of the taxon-specific comparison mode in the new MyMBGD interface, where strains of Staphylococcus aureus including five draft genomes and 48 complete genomes are specified for comparison (Figure 4A). Here, these draft genomes include strains D30 and 930918-3, which have been investigated as models for nasal carrier and noncarrier strains, respectively (20). S. aureus is a versatile human pathogen and its infection in hospitals and the emergence of drug-resistant strains poses a worldwide problem. Comparison of these two strains is interesting in terms of infectious mechanisms because the presence of S. aureus in the nose increases the risk of its infection (21). After ortholog clustering among these genomes is completed, occurrence (presence/absence) pattern analysis can be conducted on the cluster map page; in this example, ortholog groups included in the D30 strain but not in the 930918-3 strain are extracted and displayed (Figure 4B). For some ortholog groups in which a user is interested, a detailed analysis can be conducted using any functionality in MBGD. In this example, by selecting a particular occurrence pattern (indicated with ‘x’ in Figure 4B), one can identify a transposon-like cluster carrying several genes including a FtsK/SpoIIIE family protein and TraG protein, which was listed as an interesting observation by the original authors (20). The arrangement of these genes in each chromosome can then be compared on the genome region map comparison viewer (Figure 4C).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan uchiyama@nibb.ac.jp.

Show MeSH
Related in: MedlinePlus