Surveying Saccharomyces Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis

BLASTX comparisons of protein coding sequences included only the highest scoring pair in most cases. Additional HSPs were included only if the S. cerevisiae encoded proteins were adjacent on a chromosome and could be spanned by a sequence read (123 of the sensu stricto sequences and 104 of the sensu lato and petite-negative sequences aligned to adjacent proteins). Sensu stricto comparisons were performed with a PAM matrix of 40 whereas sensu lato and petite-negative comparisons used the default BLOSUM62 matrix. Several additional alignments could be generated using alternative matrices (such as PAM120) and altered GAP penalties, but essentially equal numbers of alignments were generated using less stringent matrices since these parameters often miss short alignments near the ends of the proteins. The seg and xnu filters were used to mask low complexity protein coding regions. Essentially all of the alignments are significant when the filters are used.