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Custom Tracks - Coordinate Systems

Chromosome Coordinate-based Data

Chromosome coordinates are the easiest to work with since features may be annotated across clone boundaries. However, this coordinate system is unstable and will change with each new genome sequence assembly build. Therefore, if you use chromosome coordinates for uploaded data you will have to delete the data source and re-upload it in the new coordinate system every time the genome sequence assembly is updated.

BAC Clone Coordinate-based Data

BAC clone coordinates are more stable across genome sequence assembly builds, provided the clone version number has not changed. However you cannot annotate features that span the boundary of two clones, although you can create "split-features" that annotate portions on two or more clones.

Please provide coordinates on finished clones only, for which a single contig sequence spanning the full clone length is available. If you provide data on unfinished clones, which contain more than one contig sequence, they will be ignored.

First enter any chromosomal and/or clone coordinate data you wish to display in the same tab-separated column format, as explained in the section above.

Next you must provide a list of clones you have annotated without version suffixes, their type, usually just "Clone" and their total lengths in base pairs. This information needs to appear below the feature data and separated from it using the special heading "[references]" on a line of its own.

eg:

Similarity  AL137655.1.1  homology  wutblastn AP000869.2  4260  4340  + . 373.0000
Similarity  Hs.326048.2 homology  wutblastn AP000869.2  5406  5534  + . 373.0000

[references]
AP000869  Clone 159840

AP001267  Clone 239314

Note: The [references] section must appear last in the file, after all features.