In GC Frame plot, the color code for the three reading frames on the reverse (on complementary) sequence follow the same order (R-G-B). However, it is now counting from the last nt backward, the first (-1) frame may not correspond to +1 on the forward strand. Which reading frame gets which color all depend on the length of the sequence. Adding one nt would change them all. Adding multiple of 3 will not. You have not misinterpreted.
I wish Kim would do something to help us in this regard, perhaps matching the colors of the Frame Plot curves to the corresponding reading frames below.
Carton Chen
On Thursday, January 16, 2003, at 10:08 AM, Hershberger, Doug (CD) wrote:
When interpreting a codon usage plot, it is useful to know which line corresponds to which reading frame in the Overview and DNA views. On the forward strand, it seems that this is pretty reproducibly Red - Top, Green - Middle, Blue - Bottom. However, on the reverse strand it seems to vary. Is this desirable in some way? I think that it would be most useful to have it be consistent.----------------------------------------------------
Or am I just misinterpreting the whole thing?
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Doug Hershberger
Bioinformatics Specialist
The Dow Chemical Company
(858) 352-4515
[EMAIL PROTECTED]
Computers work. People think.
Carton W. Chen, Professor
Institute of Genetics
National Yang-Ming University
Shih-Pai, Taipei 112
Taiwan
Fax: +886-2-2826-4930
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