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

FEBS Letters

Bolotin-Fukuhara, Monique²  Souciet, Jean-Luc³  Casarégola, Serge¹  Dujon, Bernard⁴  Aigle, Michel⁵  Bon, Elisabeth¹  Potier, Serge³  Lépingle, Andrée¹  Wésolowski-Louvel, Micheline⁶  Neuvéglise, Cécile¹  Gaillardin, Claude¹  Ozier-Kalogeropoulos, Odile⁴  Malpertuy, Alain⁴  Tekaia, Fredj⁴  Durrens, Pascal⁵  Blandin, Gaëlle⁴  de Montigny, Jacky³  Llorente, Bertrand⁴  Toffano-Nioche, Claire² 

[1] Collection de Levures d'Intérêt Biotechnologique, Laboratoire de Génétique Moléculaire et Cellulaire (INRA UMR 216, CNRS URA 1925) INA-PG, BP 01, F-78850 Thiverval-Grignon, France;Institut de Génétique Moléculaire (CNRS/UPS UMR 8621), Batiment 400, Université de Paris Sud, F-91405 Orsay, France;Laboratoire de Génétique et Microbiologie (ULP/CNRS UPRES-A 7010), Institut de Botanique, 28 rue Goethe, Strasbourg Cedex, France;Unité de Génétique Moléculaire des Levures (URA 2171 CNRS and UFR927 Univ. P.M. Curie), Institut Pasteur, 25, Rue du Dr Roux, F-75724 Paris Cedex 15, France;Laboratoire de Biologie Cellulaire de la Levure, IBGC, 1 rue Camille Saint-Saens, F-33077 Bordeaux Cedex, France;Microbiologie et Génétique (CNRS/UCB/INSA ERS 2009), Bat. 405 R2, Université Lyon I, F-69622 Villeurbanne Cedex, France

关键词: Alignment;    Contig;    Mitochondrion;    Ty;    Plasmid;    rDNA;    tRNA;    Protein;    Genetic code;    RSCU;   

DOI  :  10.1016/S0014-5793(00)02274-2

学科分类：生物化学/生物物理

来源: John Wiley & Sons Ltd.

【 摘 要 】

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.

【 授权许可】

Unknown