title: Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.
abstract: The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were 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 code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.
authors.affiliation: Unité de Génétique Moléculaire des Levures (URA 2171 CNRS and UFR927 Univ. P.M. Curie), Institut Pasteur, Paris, France. tekaia@pasteur.fr
authors.forename: F
authors.initials: F
authors.lastname: Tekaia
authors.forename: G
authors.initials: G
authors.lastname: Blandin
authors.forename: A
authors.initials: A
authors.lastname: Malpertuy
authors.forename: B
authors.initials: B
authors.lastname: Llorente
authors.forename: P
authors.initials: P
authors.lastname: Durrens
authors.forename: C
authors.initials: C
authors.lastname: Toffano-Nioche
authors.forename: O
authors.initials: O
authors.lastname: Ozier-Kalogeropoulos
authors.forename: E
authors.initials: E
authors.lastname: Bon
authors.forename: C
authors.initials: C
authors.lastname: Gaillardin
authors.forename: M
authors.initials: M
authors.lastname: Aigle
authors.forename: M
authors.initials: M
authors.lastname: Bolotin-Fukuhara
authors.forename: S
authors.initials: S
authors.lastname: Casarégola
authors.forename: J
authors.initials: J
authors.lastname: de Montigny
authors.forename: A
authors.initials: A
authors.lastname: Lépingle
authors.forename: C
authors.initials: C
authors.lastname: Neuvéglise
authors.forename: S
authors.initials: S
authors.lastname: Potier
authors.forename: J
authors.initials: J
authors.lastname: Souciet
authors.forename: M
authors.initials: M
authors.lastname: Wésolowski-Louvel
authors.forename: B
authors.initials: B
authors.lastname: Dujon
mesh_terms: D000595:Amino Acid Sequence; D001203:Ascomycota / Q000235:genetics*; D001330:Electronic Data Processing / Q000379:methods; D015723:Gene Library; D005815:Genetic Code; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017386:Sequence Homology, Amino Acid