Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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mathematically_defined_repeat

SO:0001642

Definition: A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.

Comments and references

Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).

Definition references: SO:jestill

Synonyms

ScopeValue
exactmathematically defined repeat

Identifiers and subsets

Accession: SO:0001642

Persistent URL: http://purl.obolibrary.org/obo/SO_0001642

Alternate IDs: None

Subsets: None

Cross references: None

History summary

Term history is reconstructed from the Git-era ontology files by comparing ontology classes across revisions. Earlier SVN-era changes will be added at a future date.

First seen in Git-era editable history: 2016-12-05 in commit 92e3cae

Most recent Git-era change: 2016-12-05 in commit 92e3cae

Number of changes: 1

Ontology neighborhood diagram

Ontology neighborhood for SO:0001642 Ontology neighborhood graph for SO:0001642 mathematically_defined_repeat. Parent, child, and related nodes can be activated to open their term pages. SO:0001410 experimental_feature SO:0001410 experimental_feature SO:0001642 mathematically_defined_repeat SO:0001642 mathematically_defined_repeat
The local DAG shows nearby parent, child, and related terms. Each node links to its own term page.

Relationships

Parents

Children

None recorded in the current release neighborhood.

Change history

This timeline summarizes changes identified in SO’s GitHub commit history, including updates to labels, definitions, parent terms, synonyms, subsets, and obsoletion status. It is a best-effort reconstruction and may not include every change to a term. Since only history from GitHub is included at the moment, any term added before the migration from SVN to Git will show as being created in 2016. This will be addressed once SVN history is incorporated.

DateChangeSummaryEvidence
2016-12-05createdTerm introduced into the editable ontology history
Initial label: mathematically_defined_repeat
Initial definition captured.
Initial parent: SO:0001410
92e3cae