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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.

-lufang-

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 ftp://ftp.genome.jp/pub/kegg/genes/organisms/sce/. In that folder is a file called "s.cerevisiae.nuc", which has the DNA sequences for all the genes in this organism.

-HomeBrew-