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Archived Comments for: Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

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  1. GC% and AG% not independent

    Donald Forsdyke, Queen's University, Canada

    25 November 2010

    There is a reciprocal relationship between GC% and AG%.

    There are two ways to modulate (G+C)% when the total number of bases is constant; either by changing the number of G’s, or by changing the number of C’s. As (G+C)% increases, trading A for G would not affect the AG%. Likewise, trading T for C would not affect the AG%. However, if T were replaced by G, the AG% would increase as (G+C)% increases. Conversely, if A were replaced with C the AG% would decrease as (G+C)% increases.

    The latter inverse relationship is observed in bacteria (Lao & Forsdyke 2000; Mortimer & Forsdyke 2003) and eukaryotes (Cristillo et al 2001), and is extensively discussed in my textbook - Evolutionary Bioinformatics (Springer 2006).

    Cristillo, A.D., Mortimer, J. R., Barrette, I. H., Lillicrap, T. P. & Forsdyke, D. R. (2001) Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, Epstein-Barr) pyrimidine-load. J. Theor. Biol. 208, 475-491.

    Lao PJ, Forsdyke DR (2000) Thermophilic bacteria strictly obey Szybalsky's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Research 10, 228-236.

    Mortimer JR, Forsdyke DR (2003) Comparison of responses by bacteriophage and bacteria to pressures on the base composition of open reading frames. Applied Bioinformatics 2, 47-62.

    Competing interests

    None declared