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SOP for pathway inference in Integrated Microbial Genomes (IMG).

Anderson I, Chen A, Markowitz V, Kyrpides N, Ivanova N - Stand Genomic Sci (2011)

Bottom Line: The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown.In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it.Automatic pathway inference is an important initial step in genome analysis.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.

ABSTRACT
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis.

No MeSH data available.


Related in: MedlinePlus

Pathway assertion details page for the pathway Archaeal chorismate synthesis in the organism Methanocaldococcus infernus.
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f3: Pathway assertion details page for the pathway Archaeal chorismate synthesis in the organism Methanocaldococcus infernus.

Mentions: If there is at least one term missing from the pathway, there are two possibilities for pathway assignment status – unknown, and not asserted. The assignment of these terms depends on whether or not the genome has a gene with an ortholog that has the assigned function. If no ortholog has the missing function, then the pathway is assigned the status of not asserted. If an ortholog is present for the missing step, then the pathway status is unknown. Figure 3 shows an example of a pathway with status unknown. Genes with six out of the seven IMG terms involved in the pathway are present, and for the single missing term, 3-dehydroquinate dehydratase, there is an ortholog with this function. This is shown in the top table in the Evidence entry where 7/7 with orthologs is written.


SOP for pathway inference in Integrated Microbial Genomes (IMG).

Anderson I, Chen A, Markowitz V, Kyrpides N, Ivanova N - Stand Genomic Sci (2011)

Pathway assertion details page for the pathway Archaeal chorismate synthesis in the organism Methanocaldococcus infernus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368422&req=5

f3: Pathway assertion details page for the pathway Archaeal chorismate synthesis in the organism Methanocaldococcus infernus.
Mentions: If there is at least one term missing from the pathway, there are two possibilities for pathway assignment status – unknown, and not asserted. The assignment of these terms depends on whether or not the genome has a gene with an ortholog that has the assigned function. If no ortholog has the missing function, then the pathway is assigned the status of not asserted. If an ortholog is present for the missing step, then the pathway status is unknown. Figure 3 shows an example of a pathway with status unknown. Genes with six out of the seven IMG terms involved in the pathway are present, and for the single missing term, 3-dehydroquinate dehydratase, there is an ortholog with this function. This is shown in the top table in the Evidence entry where 7/7 with orthologs is written.

Bottom Line: The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown.In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it.Automatic pathway inference is an important initial step in genome analysis.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.

ABSTRACT
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis.

No MeSH data available.


Related in: MedlinePlus