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codon usage - (Mar/30/2010 )

i want to investigate the codon usage of one yeast by myself, although i can get this results from internet. if someone can tell me the basic step and the software used. i think first thing is to collect the genes from this yeast. but only this step i have no idea how to do this. if i can get all complete genes without to select tons of results from the NCBI.
please help me.


For genomes that have been completely sequenced, try KEGG (Kyoto Encyclopedia of Genes and Genomes) -- the list of organisms they have is here. Note the three-letter code for your organisim, then go to their FTP site (here), go to the "genes" directory, go to the "organisms" directory, and find the folder corresponding to the three-letter code of your organism. In that folder will be a file ending in .nuc that will contain all the ORF sequences in FASTA format for you to download.

For example, if I was looking for Saccharomyces cerevisiae, I would note from the organisms list that the KEGG abbreviation for this genome is "sce", and the FTP address for the folder containing these data would thus be In that folder is a file called "s.cerevisiae.nuc", which has the DNA sequences for all the genes in this organism.