Correct terminology to describe chromosome positions
Entering edit mode
10.2 years ago
Zhaorong ★ 1.4k

Are there any differences between the terms "position", "location", "interval" and "coordinates" with regard to describing chromosome positions?

It seems to me that "position" refers to a single nucleotide, such as the "POS" column in VCF format.

"location" seems to refer to a continuous range of positions, as is defined in Bio.SeqFeature.FeatureLocation.

Does "interval" mean the same thing as "location"?

I know this question is very general, but I cannot find the guidelines to use these terms in genomics. For example, when I write a class to describe the exon coordinates on a chromosome, should I call it Position, Location, Interval or Coordinate?

terminology • 1.9k views
Entering edit mode
10.2 years ago

Positions, locations and coordinates are effectively synonyms. They can all describe anything from a single base (e.g., chr17:12,345,678) to a region (e.g., 17p11.2), though coordinates would normally refer to base-level positions (e.g., chr17:123,456,789). An interval will always be a range of positions and never a single position.


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