cgautier@BIOMAC.UNIV-LYON1.FR (02/18/91)
Date: Tue, 12 Feb 91 22:49:00 GMT From: AJB@DLVH.DARESBURY.AC.UK Subject: Codon usage database To: Multiple recipients of <+BIONEWS@IRLEARN.BITNET> I'd be grateful if anyone could point me in the direction of such a thing. It'd make translation of orfs from nucleic acid database sequences much easier. Thanks in advance Alan Bleasby SERC Daresbury Laboratory Daresbury Warrington WA4 4AD UK Email: AJB@DLVH.DARESBURY.AC.UK
cgautier@BIOMAC.UNIV-LYON1.FR (02/18/91)
answer to codon usage database It is relatively easy to construct codon usage for a species from data bank as EMBL or GenBank. Some software do that nearly automaticaly. However this have a biological significance only for species having an homegeneous codon usage (well known case are E. coli (see work of IKEMURA) Y. saccaromyces (the same author) D. melanogaster (work of P. Sharp)). For many species like mammals most viruses no "mean codon usage" exists and several strategy exists inside the same genome. This invalidate methods using an overall codon usage for CDS detection (in my opinion at least!) C. Gautier Univ Lyon I cgautier@biomol.univ-lyon1.fr