This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Correct terminology to describe chromosome positions

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
• 2,291 views • link
updated by Ram Ram • written by Zhaorong Zhaorong

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this