Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: An environmental signature for 323 microbial genomes based on codon adaptation indices. | Open Access Research An environmental signature for 323 microbial genomes based on codon adaptation indices Hanni Willenbrock Carsten Friis Agnieszka S Juncker and David W Ussery Address Center for Biological Sequence Analysis BioCentrum-DTU The Technical University of Denmark DK-2800 Lyngby Denmark. Correspondence David W Ussery. Email Dave@ Published 07 December 2006 Received 28 July 2006 Revised 20 September 2006 Genome Biology 2006 7 R1 14 doi gb-2006-7-12-r114 gy g Accepted 7 December 2006 The electronic version of this article is the complete one and can be found online at http 2006 7 12 R1 14 2006 Willenbrock et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background Codon adaptation indices CAIs represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here we evaluate and compare two very different methods for estimating CAI values one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias. Results The level of correlation between these two CAI methods is a simple and intuitive measure of the degree of translational bias in an organism and from this we confirm that fast replicating bacteria are more likely to have a dominant translational codon usage bias than are slow replicating bacteria and that this translational codon usage bias may be used for prediction of highly expressed genes. By analyzing more than 300 bacterial genomes as well as five fungal genomes we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to
