<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Some rules on gene recognition and ORF organization in the <italic>Saccharomyces cerevisiae</italic> genome are demonstrated by statistical analyses of sequence data. This study
includes: (a) The random frame rule—that the six reading frames W1, W2, W3,
C1, C2 and C3 in the double-stranded genome are randomly occupied by ORFs
(related phenomena on ORF overlapping are also discussed). (b) The inhomogeneity
rule—coding and non-coding ORFs differ in inhomogeneity of base composition in
the three codon positions. By use of the inhomogeneity index (IHI), one can make
a distinction between coding (IHI &gt; 14) and non-coding (IHI ≤ 14) ORFs at 95%
accuracy. We find that ‘spurious’ ORFs (with IHI ≤ 14) are distributed mainly in
three classes of ORFs, namely, those with ‘similarity to unknown proteins’, those with
‘no similarity’, or ‘questionable ORFs’. The total number of spurious ORFs (which
are unlikely to be regarded as coding ORFs) is estimated to be 470. (c) The evaluation
of ORF length distribution shows that below 200 amino acids the occurrence of ATG
initiator ORFs is close to random.</p>
[]
Comp Funct Genomics. 2003 Jun; 4(3):318-328