[EMBOSS] newcpgreport

[Peter Rice]

Staffa, Nick (NIH/NIEHS) wrote:
> I have been using EMBOSS newcpgreport by
> Rodrigo Lopez (rls © ebi.ac.uk)
> 
> I may be very dull and unimaginative, but I'd sure like a more detailed
> explanation of what the program is doing to define a CpG island.
> Does anyone know where this might be found?
> Or even the code.

The code is included in EMBOSS (as emboss/newcpgreport.c)

The original reference for the CpG island criteria is in the paper 
listed in the "references" section of the newcpgreport documentation.

Larsen F., Gundersen, G., Lopez L., Prydz H. "CpG island as Gene Markers 
in the Human Genome" Genomics 13:1095-1107 (1992)

If memory serves, this refers to earlier work by Gardiner-Garden.

If you need more information I am just along the corridor from Rodrigo's 
office ... once we're both back after Xmas :-)

Hope that helps,

Peter