adaptation of the short intergenic spacers between co-directional genes to the shine-dalgarno motif among prokaryote genomes适应之间的短基因间的间距器co-directional shine-dalgarno图案在原核生物基因组的基因.pdfVIP

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adaptation of the short intergenic spacers between co-directional genes to the shine-dalgarno motif among prokaryote genomes适应之间的短基因间的间距器co-directional shine-dalgarno图案在原核生物基因组的基因.pdf

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adaptation of the short intergenic spacers between co-directional genes to the shine-dalgarno motif among prokaryote genomes适应之间的短基因间的间距器co-directional shine-dalgarno图案在原核生物基因组的基因

BMC Genomics BioMed Central Research article Open Access Adaptation of the short intergenic spacers between co- directional genes to the Shine-Dalgarno motif among prokaryote genomes Albert Pallejà*, Santiago García-Vallvé and Antoni Romeu Address: Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Catalonia, Spain Email: Albert Pallejà* - albert.palleja@urv.cat; Santiago García-Vallvé - santi.garcia-vallve@urv.cat; Antoni Romeu - antoni.romeu@urv.cat * Corresponding author Published: 18 November 2009 Received: 23 March 2009 Accepted: 18 November 2009 BMC Genomics 2009, 10:537 doi:10.1186/1471-2164-10-537 This article is available from: /1471-2164/10/537 © 2009 Pallejà et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may influence the stop codon usage or the spacing lengths between co-directional genes. Results: The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy