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Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation
Author(s) -
Tekaia Fredj,
Blandin Gaëlle,
Malpertuy Alain,
Llorente Bertrand,
Durrens Pascal,
Toffano-Nioche Claire,
Ozier-Kalogeropoulos Odile,
Bon Elisabeth,
Gaillardin Claude,
Aigle Michel,
Bolotin-Fukuhara Monique,
Casarégola Serge,
de Montigny Jacky,
Lépingle Andrée,
Neuvéglise Cécile,
Potier Serge,
Souciet Jean-Luc,
Wésolowski-Louvel Micheline,
Dujon Bernard
Publication year - 2000
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(00)02274-2
Subject(s) - contig , genome , annotation , computational biology , sequence analysis , genome project , alignment free sequence analysis , biology , sequence (biology) , sequence alignment , multiple sequence alignment , genetics , redundancy (engineering) , dna sequencing , scripting language , computer science , gene , peptide sequence , programming language , operating system
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.