Sequence asymmetry as a parameter indicating coding sequences in Saccharomyces cerevisiae genome

We have compared a symmetry in purine and pyrimidine occurrence in different codon positions of coding, presumably coding and noncoding sequences of the whole genome of S. cerevisiae. We have shown that there is a very strong asymmetry in sense versus antisense strand in nucleotide occurrence in the first and second positions in codons. Since the observed asymmetry results from specific composition of the first two codon positions - the parameter is not correlated with Codon Adaptation Index (CAI) and this property could be used as an independent parameter discriminating Open Reading Frames (ORFs) as coding sequences. We have also estimated the number of presumably coding ORFs in the S. cerevisiae genome as 4718 (without interrupted genes). This approximation has been done for all ORFs longer than 100 codons identified in the yeast genome. The same method of approximation performed for ORFs published by SGD program (after selection made before publication of the data base) gave the total number of 4691 coding ORFs. That means: a - the previously suggested number of coding ORFs is overestimated; b - some ORFs discarded by the first selection could be coding (if we assume that there is any significant difference between the two results cited above); c - the method of estimation is, at least roughly, correct since it eliminates more than 2700 noncoding ORFs from our database and about 1400 ORFs from the published SGD, leaving discrepancy for only 27 ORFs and resulting in almost the same number of coding ORFs.