Alternative splicing convention
I am reading the SUPPA2 github page and can't truly understand the symbolic conventions for the events. What is a dash and what is a colon? Do they have distinct, constant meanings? For skipping exons (e1-s2:e2-s3) colon seems to mean SKIP, while for alternative 5' it means OR, and for some others like retained introns - and : seem to have the same function. Is there a well-known convention explaining splicing events?
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Figures 3 and 4 at https://github.com/comprna/SUPPA
I am asking about those two figures.
Ah. I misunderstood your question.
:is usually used to separate betweenchr,locations, andstrandfor coordinate, and-for start and end positions, but no convention for coordinate system to indicate a splicing event. Internally, we use multiple coordinates for each event: intron-based (spliced junctions) and exon-based. This is to make copy-and-paste into the genome browser easier. I believe SUPPA uses colon for everything to ease systematic parsing and to reduce redundant positions.AFAIK there is no well-known convention. In fact, I was quite confused as Oncotator (the tool where I saw the
e1,e2conventions) usese1to denoteexon-1and notend-1.In this particular case,
:seems to be a random delimiter like a comma. If you were to represent each start and end point as a vertex in a graph, hyphens would denote edges and colons would separate edge-notations.