Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

The primary analysis of the sequences for our Hemiascomycete random sequenc e tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written sc ripts and computer visualization routines, Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then agai nst protein sequences from other completely sequenced organisms and, finall y, against protein sequences from all other organisms. Blast alignments wer e individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species,validated alignments were used to infer the proper genetic c ode, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cervisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences, Annotated sequence s a ere submitted to the EMBL database, and the general annotation tables p roduced ser, ed as a basis for our comparative description of the evolution , redundancy and function of the Hemiascomycete genomes described in other articles of this issue. (C) 2000 Federation of European Biochemical Societi es. Published by Elsevier Science B.V. All rights reserved.