Defining ORFs and ORF annotation are critical. Since most of the ORFs are only proposals based on DNA sequence analyses without further supporting data, e.g. expression analyses, protein sequences etc., different interpretations are possible. This is particulary true for defining the start codon (ATG, TTG and GTG are possible candidates) and may explain some differences in length of orthologous genes in M.genitalium and M.pneumoniae.

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